Fans disagreeing is consistent with my hypothesis. To find out if there's something to it, one would have to draw and synchronise the same episode twice, let both versions be watched and the plot be rated individually. See how much of an impact it makes. (Too bad that would be way too expensive) Until then, it's just your guess against mine. I can call your Mary Sue theory bs just as easily, and point out a show where there aren't any Mary Sue characters that however isn't really popular at all. I don't think that's very useful.
Some previous MLP cartoon generations looked similarly cute, such as [URL=
http://www.youtube.com/watch?v=9ZpurerF2HM]this[/URL], the main difference seems to be that current MLP characters seem a bit older. So maybe that's an important difference? I don't know, there might well be more to it. Although, I seriously doubt the popularity of MLP can be explained by the plot just being that damn great alone. That just doesn't seem realistic to me. Yea, it having turned into an internet fad is a big factor, but then why did it turn into one in the first place?
Most importantly, why don't females like the show just as much? They don't see how great the plot is? Doesn't seem very likely to me. There has to be something that interests/excites males specifically.