I have to agree that I don't like the use of "MOTU" as a name for the heroes. As Val said, it sounds very egotistical. In the MYP series, when He-Man says "You are brave warriors, Masters of the Universe all" I was scratching my head. It sounded a bit pompous. Especially because everything in the MYP series completely left out the "universe" aspect of the property. Everything was stuck on Eternia! There was no outer space conflicts or anything. How would the good guys know they are the MOTU if they never interact with anything beyond their own planet?
Personally, I love the way "MOTU" was used in the opening narration of the 87 movie:
"At the center of the universe, at the border between the light and the dark stands Castle Grayskull. For countless ages the Sorceress of Grayskull has kept this universe in harmony. But the armies of darkness do not rest, and the capture of Grayskull is ever-most in their minds. For to those that control Grayskull will come the Power. The power to be supreme, the power to be almighty, the power to be Masters of the Universe!"
I think that opening narration will always be my favorite "canon" so to speak.
It sums up the struggle perfectly and puts the control of Grayskull on a universal scale. No one person or group are the MOTU yet, but they could be.