I would love to so the commonswealth! and the institute! maybe find out the orgin of the super mutants and find the absolute end of the enclave! that would rock! It would be kinda cool if you could chose a race in it as well you know! like: Human, alien or ghoul! all with their special abilties and factors!
Humans: allmost everyhuman living is now under the protection of the brotherhood of steel, living in seetlements all over the world the human race are begining to rebuild and repopulate the earth, the brotherhood are still searching for technology that can help them but are more focused on protection now.
Alien: a group of aliens have become stranded on earth, joining forces with the enclave they hope to take the earth for their own since they cannot return to their own planet. Enemies of the brotherhood of steel, the supermutants and all ghouls the alien themself suports the enclave and their goals and ideals of a new brighter tommorow!
Ghouls: Ghouls are ex-humans living in underground cities all over the world! they are unfriendly with the brotherhood of steel and the enclave and have therefore made their own military force... (I got no idea for a name xD) and with the low tech power armor they have (the old fashioned one, from the you gotta shoot em in the head quest) they are a small but powerfull rebellion against the human, they are also nutreal with the supermutants, meaning they will not open fire to ghouls unless the ghould itself attacks, feral ghouls are also friendly with them.
Imagine the possibilities! 3 different main-quest lines! I might just be way over my head here but I would really love that!