MGibster
Legend
The problem I've had with factions, in every game I've read or played that had them, was that every faction had a tendency to treat anyone who didn't join up as an enemy. If you don't like any of the factions presented to you, you are treated as an enemy by all of them and you end up ground to a fine paste between them. Also, if the game is about the PCs' stories, it can feel as though factions are a way of imposing the GM's story onto the game--this is probably more my reason for not using them as a GM than anything I can point to as something I've experienced as a player.
Imposing their story onto the game is one of the fundamental jobs of the dungeon master. But it's a collaborative effort wherein the DM sets up the context in which the PCs stories will be told. i.e. I arrange the pins and you knock them down however you choose. So regardless of whether the game has factions or not, if I put down some pins and you tell me you don't want to bowl, we've got a problem. If you dislike factions that much it's probably best if we select another game.