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The problem with FiM is simple, folks: it's good.
Cartoons have reached a stale point where they just recycle concepts over and over, use cheap animation and rely on shock value to reel in some people.
My Little Pony: Friendship is Magic is a cartoon that learned from the MASSIVE flops of the two previous MLP cartoons and showed everyone how to make a good remake of an 80's cartoon without failing in the process.
Instead of having loads and loads of characters, they just picked a few and gave them good, different personalities that can be used to move the story. They also picked a new, original visual aspect instead of reusing the old ones, so this show could stand on it's own.
Funny scripts with a few twists to keep people interested and avoiding 80's clichés like the plague, plus some subtele pop culture references and some dirty jokes hidden here and there helped too to make people realize this cartoon is completely different than any other "girly" cartoon made so far as well.
So basically, FiM's problem? Plain and simple: It makes other cartoons look bad.