MGO doesn't work because it's too "Metal Gear?" I don't think there's much point in making a multiplayer mode if it doesn't have anything in common with the single-player mode. You might as well make a completely different game, and not bother calling it "Metal Gear." IMO the clean slate should wait until MGS5 (or whatever it will be called) after Kojima leaves and finishes the current story.
MGS5 could not start from a clean slate. The only thing that could be rebooted is the story, but gameplay-wise it would have to remain rather close to the MGS games. I would be extremely surprised if MGS5 could grow the fanbase significantly. Especially if many jump out at the conclusion of the MGS story in MGS4. Kojima said that he has basically shown how to make an MGS game over the years, and now he can move on and leave other people use that foundation to make theirs, a lot like how James Bond movies are produced (his words).
MGO is the perfect opportunity in my opinion.