I can't imagine how much atmosphere would be ruined by multiplayer in a Bethesda game.
It would probably suffer in the same as NwN did with its fetch quests. You'd get those droll regulars who join up, power up, and know the game backwards. They'd sit around using the game as a glorified chat room whilst holding onto a key item so that a quest couldn't be completed to move the game on. I suppose it depends on the server setup for multiplayer. Fallout 3 would turn into Neverwinter Nights because it has the GECK. So even if there were armour and weapon restrictions for certain servers like for RP, you could probably bypass them by creating your own, as with NwN. Things like decorating your home and stuff you'd probably do offline, with the save from the multiplayer game you were having. I played with a lass in Michigan who was a random contact on Messenger, all through Neverwinter Nights and its EPs, and it was her first go on an RPG. Was good fun.
As somebody said in the other thread, having a mulitplayer option on a single player game would just draw in more of a crowd, because not having it can put some players off. As long as the single player element has had as much attention as FO3has had, and the muliplayer was lacking because it had been pasted onto it, I wouldn't mind so much. As long as it worked. Done properly it would be okay, and if you could find a decent group of players. The thing about that is though, that group is generally people you know, so you had may as well just set up a LAN game. lol