@Kusang: I don't know about animations, so I can't test that. But from the image, Flash's hands are a bit too small, especially when comparing to the other guy.
Incoming rant. If you don't want to read it, just look at the awesome gif below and ignore the rest of this post.
Mary Sue has a very wide range of meaning, but one of them is "a character that never has to deal with realistic consequences". Fluttershy fits this very well, because she almost never receive any kind of backlash. The most recent, prominent example is Bats!: Suggesting an unrealistic option to deal with vampire fruit bats even though she has no knowledge of them? Still become the right one in the end.
Also, a lot of times, Fluttershy developed backwards. In Dragonshy, she was willing to stand up to a dragon for her friends. In Stare Master, she ran into the Everfree, at night, to look for the CMCs. Then later, in Magic Duel, she wasn't willing to go into the Everfree even though all of her friends and the entire town was at stake. More recently, in Power Ponies, her friends being in danger didn't trigger her, but when a firefly got flicked she went berserk.
But the worst part, IMO, is that almost every episode about Fluttershy has been about her trying to be more assertive, one way or another. The recent lesson of "being too kind" is still her trying to be assertive enough to refuse the Breezies. Even the writers seem to realize this, and as a result, the only way they could make her interesting recently is gimmicks. Flutterhulk, Flutterbat, Flutterguy, Breezies. She just can't carry an episode by herself anymore.
The other case of a weak character is Applejack. She is quite satisfied with her job, and doesn't seem to have any dream other than raising money, and her only issue - being stubborn - has already been dealt with in her first episode. Being the straight mare she is ("I didn't learn anything. I was right all along"), she is not that interesting by herself. To solve this, she has mostly been paired with other ponies, usually her family, and it still works well enough, though I wish they would pair her with the mane 6 more instead of the Apple family. AJ was great in Simple Ways.