The only pre-existing factions I want to see is a small presence of Lyons Brotherhood. Maybe have some Enclave Remnants stuff, they shouldn't exist as even a minor power.
As for the Institute I want them to downgrade their ability to make Androids, the one in Fallout 3 was far far too advanced.
A couple years ago I had some pretty descriptive stuff for a Fallout game in Philadelphia and I am tempted to dig it out and post it.
Edit: This is from October 2011 and was more organized when I first made it. It is hard to believe that it was almost 3 years ago when I typed this all up.