However, if you don't want to play through all the factions, then just pick out one, I think. I agree with the overall idea of moar choices though.
I think this only applies if there is some sort of inter-faction conflict going on.
God forbid, if the College of Winterhold, the Companions, the Thieves Guild, the Dark Brotherhood and the Arena are all super compartmentalized like they were in Oblivion, then there's really no point to limiting anyone from joining all of them, or, over the course of a long playthrough, becoming master mage, then master thief, etc., if that's what someone really wants to do.
However, if the Companions and the College of Winterhold are in a nasty inter-faction feud, for example, that's when these choices become a lot more interesting.
I might be imagining the Civil War to be more epic than how it unfolds in the game, but it seems to me that this epic conflict is going to be an undercurrent to the guild quests. The lines have already been drawn with Windhelm serving as the Rebel base of power and Solitude as the Empire HQ. I don't think it's a coincidence that each of the three major guilds is based in the remaining big cities, Riften, Whiterun and Winterhold.
Each of the Nine Holds are going to have to take sides and each of the guilds or just about any other large organization is going to have to take sides in this war. It might play out where the PC chooses to help the Rebels or the Empire and then must win over the various guilds to support the side he chose. At least I certainly hope it's something that huge.