One reason for someone to not do something is that if they do it half-assed, then it ruins their credibility. Unless Nintendo found some magical flawless way to integrate multiple players within the context of both gameplay and story, then the game would only get panned for ruining what would otherwise have been a superlative single-player experience. Sure, the opposite was somewhat true with the original Smash Bros, but people managed to overlook that flaw because the core multiplayer mode could also be played alone. I sure wish I had a good example of shoddily-done extra features causing reviewers to bash an otherwise good game, but none really come to mind at the moment.
EDIT: Ah, I've got an example now. Deus Ex for PC. Originally it didn't come with a multiplayer mode, but through the ability of PC software to be patched, an ass multiplayer mode was released after fans clammored for it. And if you didn't catch on before, the results didn't end up so hot. Had this mode been released at launch, the scores would likely have declined a fair amount simply by weighing down the polished single-player mode with a tacked-on multiplayer option. (Okay, fine, so it was only Deathmatch, and not the Co-Op example you're probably looking for. But the principle that it needs to be done right or not done at all still stands.)