Thirding the regret for losing the explorable map in Geneforge, with its possibility of finding areas too early and getting yourself into trouble. And on the same note, adding the possibility of finding hidden passageways etc. without asking the right person -- maybe only if you have a tracker with you? -- would be nice. This way broke the suspension of disbelief for me, by requiring the use of metagame reasoning.
The other thing that we were missing from Geneforge was the option for making charisma checks. Man, that was satisfying, when you could sweet talk someone from near-hostility into being helpful and giving you directions.
Also, I was continually annoyed by the lack of a nonlethal damage option; I know this isn't new, but it was more significant in this game. Miranda and Redbeard are always telling you to bring people back alive for questioning, but not a single person in the entire game ever came quietly. OK, perhaps that's a testament to the fearsomeness of Avadon's "enhanced interrogation techniques". But why on earth is it impossible for someone on your team to knock someone out and tie them up?
On the other hand, I did like the simplified skill system, and loved these huge maps for all the areas!
ETA: also, the junk bag, which removes a huge amount of the annoying inventory management issues.