It's probably already been said, but one of the biggest factors is probably camera issues.
Games like this where co-op works well; Streets of Rage, Castle Crashers, Golden Axe etc, have a single fixed camera view and are '2.5D'.
To make it work well in a fully 3D game would probably require a lot of effort, building the game for this sort of play, a simple tacked-on co op mode on something like bayonetta probably wouldnt work very well because the game was designed around single player.
It would almost definately need to be split screen too because having multiple players on a 3D screen being tracked by 1 camera would just end up as a mess!