Tons of stuff:
More options in combat (less passive combat, more tactical combat, whatever)
More non-linear
REMOVE THE DAMN MINIGAMES!!!
More role-playing opportunities
More action/reaction
Less annoying NPC interactions
More head models
More interactive environments (at least add stuff like jumping, swimming, etc.)
Balance out melee/ranged
Less clunky inventory system... actually, completely reworked interface
Okay, this will never get in, but if the game is actually turn-based I'd be thrilled