If I played co-op with someone, would it be in my version of the commonwealth or theirs? Or a third "open" one which has no bearing on mine or theirs?
Because of how specific and different everyone's commonwealth is, it would be impossible for you and a friend to exist and interact with the game in the same world.
We have a thread for discussing multiplayer in Fallout games: http://www.gamesas.com/topic/1581454-fallout-multiplayer-discussion-thread/page-2