There are two ways I think a choice system can work in a game.

1) The Route of something like New Vegas, (New Vegas I feel handles this way better then Skyrim). You have an insane amount of things one can do, and you can get radically different endings. It's far more then a simple 'good or evil' choice, and you see the ramifications of all your actions.

2) The route of games like Agarest War. The choices you make are always toward the same goal, but it's more in how you do it. Are you going to be a bit more cold hearted and pragmatic with your decisions? Are you going to try to be the goody goody? All the choices available can fit your character fine, so it's a very limited range of your characters actual personality, but it helps build relationships with characters and in a few instances determine who you can get to join you.

So basically I only find the two extreme ends of choice making enjoyable, minimalistic or over board. I don't fancy the in between ones to much.