I think it would be pretty cool if they didn't make groups as black and white as bethesda has been doing recently specifically with the Thalmor of Skyrim, Caesar's Legion of F:NV, and and Enclave of nearly every fallout game save for F:NV. The idea of a group based around discipline, reliability, and rigid structure with tribal roots sounded really cool...but how evil they made Caesar's Legion was just ridiculous. I am a huge fan of making tough choices and having games that allow for people to choose sides in a conflict, but I would like it to be more difficult then crazy slavers and the republic trying to protect everyone.
Also a bigger focus on plot. I loved the variety of things you can do in F:NV but the stories/quests were very bland. I love FO:3 just because of the main quest. I want a long spanning quest that is a bit more gripping...or at least something more then "you got amnesia, now decide the fate of New vegas"