Fallout 3, similar to earlier Bioware games had quite a few choices to make but a lot of them were quite clear cut "evil/good."
I'd like to see more quests that involve choices that aren't just simply cut and dry good or bad, but things that might unfold unexpectedly. Maybe one of the characters lied to you, maybe things just didn't play out how you expected, maybe there really isn't just a good "Right or wrong" answer to the choice you have to make in a quest.
I also hope that the consequences for what you choose aren't simple but rather things that have a lasting affect, even an early choice in the game might have a ripple effect that comes back much later.
The conequences for your actions shouldn't be immediate (IE you shouldn't be able to simply save your game, make your choice, then play 5 more minutes to see "what happens" but rather you make a choice and the consequences are long lasting and the affect your choices have might not be felt until much later in the game.