I decided to make a little "Contents" so you dont have to go searching through this book of a post...
1. More Landmass
2. Items to Add
3. Balancing (Very Short)
4. Suggestions For Android
5. Suggestions For Alien
6. Suggestions For Werivar (Psi's)
7. Suggestions For Soldier (Skills)
8. Pro's and Con's, MiniMods
9. Smart AI
10. New Droids
11. Minibosses
1) More landmass. There's a lot already, but MORE... it's like cookie monster on crack... and... he's craving landmass instead of cookies... or crack... ... ... nevermind what I just said there. What I'm trying to say is I suggest adding yet another map that resembles a Villa Corp Planetary Center. The Planetary Center is much closer to the Alien Hive than the mining outpost, and because of this is being overrun by aliens. This could simply be done by making a map with a "Town" in the center, with VC spawns inside, and alien spawns along the perimeter. We all know that VC wants the aliens dead, so of course the result will be a miniature "battlefield" between the VC and the aliens. If your interested in such a thing, maybe you could even add those droid spawns that are found in the desert areas, making it a war between 3 forces on the map... well... four if you count our hero 
You might also think of adding another ice map... seeing as now there are several desert maps but only one with the biting cold. I have no suggestions as to what to -put- in this new ice map... just that I believe another one would sort of scale the game a bit better.
2) Items:
a- An item which causes corpses to dissapear after a given amount of time pases in game. The Hive sector eventually becomes littered with bodies, if your a hunter.
b- An assault rifle. combining a long metal rod with a VC pistol might be a suggestion for it's creation. Until a better graphic is made you could use the sniper pistol graphic. The assault rifle doesnt shoot as fast as the akimbo double barrel pistols, however hits for more damage per shell.
c- Grenades. Almost identical to the repair unit's blast when triggered, only using flak (bullets?). Suggestable when going up against those nasties whom take damage from physical instead of electrical damage. A suggestion for creation might be ether mixed with glass tube, or a heat packed mixed with a glass tube.
d- An organic converter. Suggestable creation would include a glass tube (or two), a replicator cell, a computer chip, a full cell, a fuel converter, and a lighter B... for turning that friendly little corpse into carbon. The organic converter could be able to turn corpses into an added point of MAX HP for all characters (minus the engineer). A great way to actually make picking up bodies useful.
e- A laser boomerang? Would probably take too much scripting... but perhaps if it were possible the item would be a weapon that hits an enemy and returns, then can be released again. The object creation would require firewood, two fuel cells, and a laser pistol. Perhaps even adding a power crystal would cause the boomerang to pierce the target... or cause a chain attack which would hit one enemy then spread to all enemies in a 45 degree angle behind it, hitting them for 1/2 damage, then spread to all 45 degrees behind them for 1/4 damage and so on to a certain distance. This chain effect would look nice even if you dont like the boomerang idea 
f- Some type of melee weapon... any really... a chainsaw? A sword? A knife? A stick? I just like swinging things... hey... it's an idea, I never said it'd be a GOOD one. 
g- Heat Boots. Let you walk over that pesky lava without takes those nasty little second degree burns! May drain your energy, however. I dont have any suggestions for creation, I just know that they will give the foot equipment box another use (other than the ether boots)
h- Airstrike. That means building an aircraft that you release, which drops bombs where you want to. Suggestable creation would mean 4 metal rods, 6 common metal, 2 precious metal, 1 power crystal, and a self powered ether generator. When combined they create a "bomber" which after being used in the inventory, dissapears. Now, when the player uses the spyglass, crosshairs can be found in the center of the screen when viewing. If fire is pressed during this time, a few seconds pass.... and then several explosions reign out in a line parallel to the player, damaging/killing those in it's path. The airstrike takes a few minutes before it can be used again.
3) Some balancing?
4) The possibility for the android to alter itself beyond simply upgrades. As a machine craving parts to make himself stronger, honestly, he wouldnt stay a warp engineer drone much longer... he'd start either wanting to become a stronger machine... a mech or a master computer... or an actual living organism... tearing the organics from living things to turn himself into a terminator type machine (like Frankenstein!). Perhaps altering the android would cause some benefits and some difficulties... IE becoming organic would give him the possibility of a food bar which must drain before his energy begins to dissapate, though his health drains faster when hit, or becoming a mech would make him be able to take more damage and give a chance of completely deflecting an attack... though his energy would fall at a faster rate. A suggestion...
5) Suggestions for the alien...
a- A little male alien companion for our alien avatar? Spoken of in her journal, we never actually -see- this male alien stalker of hers. Well maybe we could implement this fellow... at a certain level he grows into a "pet" whom inflicts a very small amount of damage, though is invulerable and is fast enough to keep up with our avatar... giving a little truth to the storyline, if you will.
b- The possibility of starting the process over for the alien. Sort of a "rebirth". When the alien reaches it's max level, perhaps it could be able to start over, with some type of a benefit... more health, or something.
c- Mind control. Being able to temporarily steer your target pet alien. Upon death (or que) control is returned to the avatar alien.
6) Suggestions for the Werivar:
a- Fury, Boiling Blood, or Rage for the Werivar... another psionic skill. This one causes time to slow for a (short) moment, perhaps 50 ticks on it's first level, and allows the Werivar to only use his claws, however during this time the Werivar hits for an enormous amount, and takes 1/4 (?) damage. Anger has never tasted so good.
b- Canine Reflexes. He runs faster, and has a greater chance of deflecting an attack. Somewhat of a secondary defense skill.
c- Growl, Howl, and Wolf. Scares, attracts or stuns enemies to, away from, or near the Werivar.
d- Carnivorian Instinct. The Werivar ingests all the bodies within it's proximity... yummy... (not my best idea, but hey, he's hungry)
7) Suggestions for the soldier:
a- Covert Operations. A skill purchaseable through the skill shop, which (after purchase) can be turned on or off. Renders the soldier undetectable by NPC's... however drains his energy while active.
b- Skilled Contruction. A skill purchaseable through the skill shop. All stationary turrets built by the soldier now do 1.5x damage. A later skill could be Masterful Construction, which would make that number rise again to 2x damage.
c- Controlled Breathing. A skill purchaseable through the skill shop. This skill makes the soldier's accuracy near perfect (guns like the pulse laser nearly always fire exactly where you aim).
d- Battle Sense. A skill purchaseable through the skill shop. It automatically aims at the closest monster within 10 degrees of the soldier's line of fire.
e- Adrenaline Rush. When the soldier reaches a given level he gets this skill for free. It slows down time as long as he is under 1/4 health, and causes his regeneration to multiply by 2x times during this period.
f- Spartan. When the soldier reaches a given level he gets this skill for free. As long as he is above 9/10 damage the an area 30 degrees wide and a few feet long behind him causes aliens to catch fire.
g- (Ammo) Ether Combine. A skill purchaseable through the skill shop. After purchase, the skill can be turned on and off. When active each bullet fired by the soldier subtracts 1 ether from the soldier's inventory, however causes explosive damage when it comes in contact with an enemy, damaging and knocking back those around it.
h- (Ammo) Crystalline Tip. A skill purchaseable through the skill shop. After purchase, the skill can be turned on and off. When active each bullet fired subtracts one crystal (the blue ones that the beacon ray uses) from the soldier's inventory, however freezes the enemy. An even stronger skill that could be dependant on this one may be (Ammo) Crystalline Round. This later skill would freeze the target and those in the target's immediate proximity, however would drain 2 instead of 1 crystal.
i- Elemental Stoicism. A skill purchaseable through the skill shop. Acid, Hot, and Cold rain all have 3/4 an effect. Healing rain has a 1.25 multiplier on how fast it regenerates. A later skill could be Environmental Stoicism. Acid, Hot, and Cold rain all have 1/2 an effect, and hot/cold weather have 3/4 an effect. Healing rain has a 1.5 multiplier, and lava hits for 3/4 it's origional damage.
j- Barbarian. A skill purchaseable through the skill shop. All damage dealt to enemies, whether melee, explosive, flammable, energy, or projectile, all regenerate the soldier by 1/8 of the damage inflicted. More pain, more gain, as they say.
8- Before the game there could be a pro's and con's sort of menu. You could chose your character to have one pro for every con selected... for instance you could pick your character to be thick skinned, taking only 9/10 their origional damage, but would have to chose a negative skill to compensate, like fast metabolism, which causes their hunger to drop by a 1.2 multiplier.
Pro's:
Slow Metabolism. That donut you ate last week is still keeping you going. (80% origional food loss rate)
Calm Headed. You make no distinction between one alien or one houndred. (richochet from being hit by others is halved, richochet by aliens attacking you and attacks hitting others is doubled)
Ambidextrous. Not only can you write with both hands, but you can tear things to shreds with them too! (Werivar and Alien both can chose this to do 25% more damage with every melee attack)
Process Master. You know how to multitask so well you are virtually a computer... who knows... maybe you actually are... (Human and Engineer combine things 25% faster)
Memorable Mind. You might have forgotten some things, but when they come back to you, you can describe them down to the smallest atom they are composed of. (Psionic combines it's abilities in 50% of the time)
Experienced. You know exactly what to do. (Begin the game with 2 levels of XP already completed)
Con's:
Fast Metabolism. You go to the bathroom so much as is, taking a laxative might cause your death. (120% origional food loss rate)
Worrier. Your not exactly a hero when you curl up in a ball and cry for your mother. (richochet for you is doubled, for others is halved)
Clumbsy. Growing up you recieved the nickname "Bodyshot" for a reason. (Werivar and Alien hit for 80% of origional damage when attacking)
Tunnel Vision. You work hard, it's a pity, though, that you can't set aside enough brain power to learn from that work. (Human and Engineer take 25% more time to combine)
Forgetful. I would put a description here... but I forgot. (Psionic takes 50% more time to put mix it's abilities)
Inexerienced. It's you first time alone... scary... (It takes 2 times as much experience to level the first two levels of experience)
You might also have abilities that arent exactly pro's or con's... but alter the way the game is played anyhow... such as:
Teammate. Without anyone else, you freak, but in a group, you excel as a leader. (With 0 friendlies in a given proximity, damage to you is doubled. With 1, it is normal, with 2 it is 75%, with 3 or above it is 50%)
Warm/Cool. When you were younger you lived in the desert/tundras. (If warm is picked the player is 50% more susceptable to freezing, but can survive in heat 50% longer before having a stroke. If cool is picked, it is the opposite with cold being the stronger trait)
Hardcore Mode. Your style: Kickin' names and takin' booty. (All creatures have 2 times more HP. a "Superhard" setting... this alteration is for the experienced looking for a challenge)
Vampire. Those two little holes on your neck might mean something. (Health does not regenerate, however killing enemies gives you 1/4 of their max HP)
9) I've made this suggestion to another mod, but while it's still fresh in my mind, I might as well put it here too. I suggest smarter AI. Some creatures might still use the old AI, simply running at you until your dead, however AI for the more intelligent creatures should be upgraded. They could duck behind objects when being fired at, strafe away from the player's attacks, and run away when they are dying. Even more advanced, they could warn their allies around them when you are spotted, attack in groups, use more than one type of attack (if you get close they try to punch), actually walk -around- impassable objects when they are on the other side of them, and react to their environment (A soldier pushed into lava screams, aliens huddle together for warmth during cold rain, when two droids run into one another they make buzzes and beeps, sharing information). If you were to take this to the limit, you could actually make the factions "hunt" the player in time. This would mean spawning groups of creatures who wonder the map searching for the player... staying in one spot during the night, and moving around until they find the player (or a sign of the player's presence, like a fire) during the day. This group would hide and try to ambush the player at times... send out scouts or "kites" to attack the player then lure him to the rest, and maybe even take military stances (I.E. walking in a formation, towards the player when they are spotted suddenly).
Anything listed above would make the game more complex than simply shooting everything near you to bits... a smarter AI would give the same some depth and even give some strategy to the carnage. AI is really tough to script, Im sure, but if it's simply making them try to dodge the player's attacks, or if it's ingeniously using mind games to confuse the player, ANY better AI would make a great update to the game.
10) New droids. The soldier's have their Snipers and BattleDroids, and the Aliens have their Dire Reapers... but what new creature(s) have the droids recieved? Maybe some saw droids... if the player gets near them, the player takes melee damage. Or statfield droids, which jam the player's weapons or abilities (minus melee) for a couple of seconds when hit with their slow-moving shotgun projectile attack. Or repair droids which attacks like a normal droid, except regenerates it's health quickly (and that of other droids in it's radius slowly).
11) Extra miniboss-like creatures that can be found around the planet.
a- A "sandworm" in the sandmine area. It has two parts, one that follows the other. The main part of the sandworm, which acts like the large "worms" found in Eden, only is seen when it comes to the surface to hit the player. This part is invulnerable. The second part, however, the tail, is visible constantly, and tags along behind the "head" of the worm. This part is what you must destroy in order to kill the worm.
b- A "predator" creature in any of the open forest areas. It wanders the map stalking aliens, killing them, and devouring their bodies. It attacks like a bull, though at times resembles the invisible "reaper" in it's charge. The creature sneaks up to it's prey, invisible (like the reaper), however when it's within range it stops, and becomes visible momentarily (also making a sound), once a moment goes by it charges toward it's prey, hitting for little damage, though with an extreme richochet. It then acts as a reaper and races to the other side of it's prey, letting it fall into it's range. When the prey reaches it's range, it becomes visible again, momentarily, and waits (much less than the last attack). Once it's quick wait is over it unleashes a deadly attack that kills it's prey. If it drops a corpse, the creature takes it and devours it, then becomes invisible, returns to a specified part on the map, and waits awhile before going out for another hunt. -IF- the player happens to -BECOME- the prey, the player must act as a bullfighter to kill the "predator"... the way this works is that the first time the "predator" becomes visible (before it's rush towards the prey), the player must hit it. This first hit causes the predator to charge in whatever direction it's facing at the time of taking that damage. The player then must sidestep the charge. When the creature becomes visible again the second time (for what it thinks will be it's deadly second attack) the player hits it again, causing it to take a decent amount of damage. This process is repeated until the "predator" is at 1/4 HP. It then retreats at it's rush speed towards that set point on the map listed above. The player can cause it's ultimate death by meeting it at this spot, and repeating the method of harming it until it dies.... It wont be as confusing or as hard to script as it sounds once the concept sinks in... trust me 
c- A "defense array room" that can be found via a ladder that heads down from the abandoned base. this small map has several walls set up which the player can get behind for defense (sort of like american gladiators, for those of you who remember the 90's), and opposite of the enterance, an array of defense mechanisms, perhaps like deployable turrets, or more ideally like the droid bosses found in the desert. A suggestable setup might look like this:
_____________________________
|......................................... O | <--Entrance
|_X__..................................___| Body + Medpacks (@ X)
|X............................................| Turret (@ X)
|......................______..............|
|...........................X..........____| Turret (@ X)
|............................................X| Turret (@ X)
|..............................................|
|____........................................|
|X........................__...............| Turret (@ X)
|..................|______.................| <- Final Wall
|..............................................|
|..X.....W...*..............*...W.....X..| Turrets (X's), Main Boss Turrets (W's), Unique Turrets (*'s)
|_____________________________|
Once all of the turrets (minus the *'s which are invulerable while the rest are still alive) have been destroyed, the player must hide behind the final wall to initiate the last sequence of the boss fight in which the unique turrets (which before fired lasers) move forwards and block in the player... on the lower half of the map it would now look like this...
.................
...........*_..
.*|______..
The lasers now fire constant steams of lasers, which are quite deadly. They take turns moving left and right, or up and down. Both momentarily turn red before they begin their scans across the area... this is a que for the player to hide behind either the outcropping infront of the left-right turret or the up-down turret. Once this laser begins its trek across the area, firing, the player can hit it while it's temporarily vulnerable. The laser returns to it's position behind the wall, and the other laser gets ready for it's trek. The boss is killed when both lasers are completely destroyed.
Again, it sounds a lot harder than it really is. If you've ever tried to play a game like The Legend of Zelda: Ocarina of Time, you would understand these concepts perfectly, seeing as I sort of based these boss concepts off of those I've came to meet in other games.
Even if you dont like the ideas, but like bits and pieces of them, remember you dont have to completely trash the entire thing. Use the concept you liked in that idea, and apply it to your own! Hey, even if my ideas arent all in all to your liking, dont let that stop you from letting them spark your own ideas you'd love to add  .
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) Killing panicked crewmembers screaming, 'We're gonna die!!' and 'An alien! Kill it!'. Oh yes, they got guns.