If you're talking about playing sides, I.E. Horde or alliance, I really doubt that you will have to pick a faction starting out at character creation. Also only those 3 factions leaves alot of factions unaccounted for... Master's Army, The BOS on the west coast and the one around Chicago, Slavers, The Khans, Caesar's Legion (I'm not sure if gamesas will use concepts from VB like Caesar's Legion) The Rangers (the real one's not the substitute from NV), The gun runners... not to mention all of the other raider gangs, vaults and settlements...
What happens to all of them? Another drunk conquistador conquering the governor's ball...