Clicking on an enemy will start combat. The characters will take turns to deal blows to each other. This is very similar to modern western RPG's, such as Knights of the Old Republic and Dragon Age.
In combat you can choose to use special melee skills. You can learn these as the game progresses, probably from certain people (zelda style) or from leveling up.
Total damage dealt is taken from the equipped weapon, so you still have an incentive to use bigger weapons. Using melee skills you can choose how to distribute the damage from the weapon, giving you a strategic benefit.
Skills may be scripted using the Driftmoon scripting language. The system could easily be used for magic as well as combat.
Some possible skills:
Berserk attack, deal plenty of damage to the enemy, but take some as well.
Stun, enemy loses next turn.
Swirling attack, damage to everyone around.
Fire attack, time based damage.
Concentrate strength to next attack.
Armor piercing attack.
Weaken enemy's shields for next attack.
Reflect next attack.
Block next attack.
So that would give you a fair bit of melee strategies. Also giving a different set of skills to enemies will make them different and perhaps more interesting to fight. If you have any new skills to add, and I'm talking about actual combat skills and not magic, I'm quite keen on hearing your ideas.
For balancing, I'm thinking of a system where it would automatically make the less frequently used skills less expensive. Any thoughts on that?