The reason is because it is insanely hard to make characters from scratch. The author has to essentially animate every possible move of the character, which ends up being hundreds of frames of animation. Most Marvel and DC characters have had their sprites ripped from other games, such as Marvel vs Capcom. Since there are no games to rip MOTU characters from, they need to be created from scratch.
I wish to see a proper He-Man and Skeletor in a fighting game one day!!