What remains to be seen of course is whether the players themselves will be able to create their own factions in-game, or exert any kind of influence and control over pre-existing factions once they join their ranks.
Existing Factions: Rising from Initiate to Leader?
In a hypothetical situation, let us say some player ends up impressing and joining the Brotherhood of Steel. Should that player be able to rise through the ranks of the BoS and, eventually, have more of a commanding role in the organization? Or should players be stuck at the grunt levels, doing missions and generally doing the bidding of their NPC masters?
Player Factions: Carving a Niche or Earning Respect
Player-created factions may have to face an uphill battle to come into existence, assuming they could be created at all. After all not only would they have to compete (in a sense) with other player factions, but also against the established ones. As some NPC factions may be able to get along, ally or at least have uneasy truces with one another (according to the lore), a similar system might have to exist for player factions as well.
Imagine if you will a reputation/karma system that exists at more than a personal level. Not only would you have your own viewed standing, but also that of whatever group you happen to be a part of as well. Fall in with a bunch of other players who like raiding caravans and cannibalizing settlers, then don't expect a warm welcome (save from a flamer) from many major settlements.
In theory player created factions should be separate from guilds/clans, as there really should be ways to form discrete groups of players as well as larger collectives (alliances/factions) as needed. Several smaller guilds who work well individually and share similar enough goals (and kind of get along) could get together and form a faction thus.
Sounds messy doesn't it?