)
Only MLP villain I recall using them (well one of the elements) was Sunset Shimmer, so that wasn't quite a recurring thing as it was in Sonic.
Frankly, that idea of "Heroes & villains fighting over magical, all-powerful rocks," has been around in video games & cartoons/anime BEFORE Sonic. In fact, Final Fantasy did it many years before Sonic even existed.
Not to mention, I don't even see proof that Lauren Faust, or many FIM staffers are "Sonic fans." Only one I can think of, is storyboarder Sibsy.