Most of the complaints about the factions just seem to boil down to "They're not likeable enough!" which I don't really get. It's a brutal post-apoc world, and I think the factions reflect that.
I hear what you are saying, but I see three reasons not to follow this:
1. I am convinced that even in a brutal post apocalyptic world there would be people who would want to fight for all of humanity (if you want it in pathetic words: for a democratic society) and not only for their personal interests or fanatic visions. So giving no choice like this is not plausible for me.
2. Even if you believe that the brutality of the world would lead to only selfish behavior, this would also include "lone wolves", who fight only for themselves and wouldn't want to join a faction exactly for that reason. In fact, speaking in game mechanics, the absurdity of not allowing this can be seen as follows: If you play the game as far as possible without joining a faction (by solving all side quests, even all factions related ones, except for those, which force you to finally join one faction; also killing all accessible enemies on the map) you get so powerful, that you could easily win the end-game by yourself. The game simply excludes you by invisible barriers (the walls around the area are low enough that you could fly over them in other areas of the game) from entering the end-game area, if you don't belong to a faction. This is lame even from a purely game-mechanical point of view.
3. With the "base settlement" (I always forget its in-game name) and the people assembling there PB have in fact modeled a "likable" faction (with a vision like the one described in 1. above). So PB themselves obviously believed that the world didn't force everybody to be an asshole. Not making this settlement a faction of its own was therefore not something unavoidable but simply lame again.
If there wasn't a faction system, most of you would be complaining that there's not a faction system.
I have no problems with or without a faction system, but only with the three points explained above.
An additional thought: If you play correctly you can convince all factions to join you in the end-fight, even those you don't belong too. I wouldn't mind, if the game would require you to convince at least two of the factions to join your fight, but without need for you to join one of them.