The difference is that Galaxy Girls actually looks good, it doesn't dig itself so deep into the uncanny valley it hits China.
Equestria Girls just looks so… meh. It's just LPS with weirdly-colored anthropomorphic characters. It doesn't even deserve to be called a 'humanization', because I certainly don't see any humans in the movie (except perhaps for Brad, who actually looks like a human just with a ridiculous hair-style).

At least the Galaxy Girls had more variety in their designs, and weren't a product of capitalizing on a popular franchise with a cheap marketing gimmick… Besides, the 'bizarre coloring' is mostly a complaint on the "humanized pony" aspect of their character designs, not just their appearance solely without that context.
And just because another one of Lauren's creations looks similar to Equestria Girls does not necessarily mean it shares the same core vision.

Now, I could be wrong about Equestria Girls (I'm trying to be cautiously optimistic), since Hasbro is probably ignoring the Brony demographic completely with it's advertising campaign… In fact, I've never had a huge problem with what the writers were faced with working with before, anyways. So whatever the result; I can at least know they tried their best. At least we can't expect it to be as bad as "Batman and Robin" as far as the effort put into it goes. Even with the cliched company-inserted plot elements in it, that does not necessarily mean it's destined to be thoroughly un-enjoyable. Granted, it's probably not going to be "Movie of the Year" or anything, but there's still a potential of satiable entertainment value if it doesn't exceed our worst expectations.