As a child, Masters of the Universe was the first stuff I ever played with. I think it'd be cool to have an RPG about them, but I don't think it can be done.
Like most shows aimed at a younger audience (mind you, I have yet to see any of the new show, so bear with me), Masters of the Universe's characters have the universe revolving around them. It's hard to have a group playing in that world when everything is revolving around He-Man and Skeletor. Throughout the series, nothing really changes. He-Man and Skeletor have their frequent clashes, but nothing is ever resolved, and no protagonists besides the ones already established emerge.
A gaming group set in that world would want to go explore, not just repeatedly throw themselves at Snake Mountain (or wherever Skeletor lives). They wouldn't be beholden to He-Man, and would soon overshadow him as they went up in level, which is off-tone for the setting. It'd be hard to justify them not getting killed when they lose to enemies (since the good guys never die in the show), and even harder to deal with it if they start killing major foes, since no new ones are available to bring in.
All in all, its a good example of what happens when you try and convert most shows, especially ones that don't go out of their way to flesh out the setting, into a RPG. It just doesn't work.