Uhm... Uhm... Uhm... I think...
Ok, large "npc" factions, representing large amounts of ressources outside the map, should be very very hard to beat completely, if not impossible. You might be able to chase them nearly out, but they'll allways be a thorn in your side.
Medium and small factions, should be possible to take over economically or "politicall"..., unless they are fundamentally philosophically opposed to you, in which case it's war, war, war until one wins nearly completely.
Factions that like you or are like you, should help you out, economically or with a contingent of factionspecific military/technical level appropriate help. Not everyone can spare powerarmors or doesn't even have access to them.
Well atleast it would be nice to have the option...
As it is, I don't know exactly how it will work, but I hope I'll be allowed to also make settlements in the name of existing factions (or that I can become a "prominent member and representation of them). In fo3 I kinda hoped I could have lead to rileys rangers to grandeur and expansion.