Retro might implement multiplayer online, and I'd be happy with that, but I really doubt that's why they delayed the game (if they did at all). I think the fact is that it's hard to finish a game in two years. Retro did it before with Metroid Prime II, but the game was a very straight sequel to Metroid Prime. They're trying more new stuff in this one, and it might take a while to get it right.
Here's another thought: Nintendo has always said that it doesn't want to repeat the game drought that we saw with the GameCube. With third parties providing at least a dozen additional launch games, and with hype really high, maybe Nintendo decided to push some of its own games back a little: give third parties a chance, and ensure that the first half of 2007 will see a few major releases.