I didn't really get into Metroid Prime: Hunters for some reason (probably a glitch since I'm absolutely sure I can't seem to reach Trace) or even its multiplayer, so I don't know how "successful" its online multiplayer mode is. If it is good at all, I don't see why they wouldn't be spending the "extra" time putting a similar or better mode in MP3. After all, Metroid Prime 3: Corruption was going to be a launch title at one point, and I believe that even if they delayed it so it wouldn't conflict with Zelda and other games, that Retro Studios wouldn't just sit on it.
Halo as a single player game is kind of lacking. (I haven't played 2, but I hear that's not quite fulfilling either.) Its strength comes from multiplayer (duh). I have trouble imagining Metroid trumping Halo, but maybe that's just because Metroid has always been a single-player experience and Halo is the most-hyped multiplayer Xbox series. But the Wii is pretty hot, Hunters might not have been too bad, Retro Studios could potentially devote ALL of their time now to make a robust and interesting online multiplayer mode, so why the heck not? It's the closest thing to a Halo-killer, however much of an uphill battle it is. I'd say it's even a safer bet than making a new franchise from scratch.
I think it's stupid that people think a solid single-player game and a solid multiplayer game can't co-exist together. Sure, resources are usually devoted to one or another, but I think however big Super Smash Bros. Brawl is, Nintendo ought to have other killer apps of other genres in their online arena, and considering how FPS-happy America is, why not put that effort into MP3:C?