I have been thinking of a few things I'd like:
1. magic items in combat
When opponents in a battle are defeated they have potions, crystals, and other items. I'd like to see opponents actually use these things against my character.
2. plot paths tied to different stats.
I'd like other stats to make alternate paths in the game, similar to how leadership works.
3. fight to the death
Having most of the opponents fight to the death is irrational. If things devolve into a fight and the opponent is critically wounded, I'd like for them to try and press for a truce or anything other than to continue to fight. Right now the options are usually limited to fleeing or fighting to the death -- and when an opponent flees they are easy to find again and press into battle. There should be a hide option.
4. hiding
Speaking of a hide option... I'd like to be able to use stealth more.
5. plot variation
For plot variation I'd like more interaction with normal characters at lower levels. It would be nice to have more side story aside from following the main plot lines. e.g. while the apprentice is getting started, he could make contacts with people by agreeing to protect a merchant on a trip, or things such as this. Make reputation more important.
6. scenario editors
I'd like for there to be an archive where people can submit maps they've made with adventures in them.