Oh boy. Where do I begin?
The Derpy Fiasco: Why these sensitive snowflakes has to change somepony that wasn't? It wasn't like Dashie saying something incredibly ableist to Derpy on purpose. Derpy is one of the most pure and beloved characters of the MLP franchise, period. The fans love Derpy for who she is. Once you change her to make her less derp, you're gonna piss off a lot of people just to please a vocal minority. It also doesn't help that the fans going after Amy Keating Rodgers for that incident (which is very disrespectful considering that she has a disabled son).
While I'm glad that Derpy still continues to live on throughout the show's lifespan, but this incident shouldn't happen in the first place.
The Twilicorn Incident: Okay, now this is most infamous incident out of all them. We all know Magical Mystery Cure and Princess Twilight and how Hasbro handle it very very badly. I feel bad for MA Larson since he become a laughingstock in the MLP community over something that he had no control over. I think it's a situation of very bad timing. Magical Mystery Cure was supposed to be the series finale and FiM was originally going to end after 65 episodes so they rerun in syndication. When Larson finished writing the final script, Hasbro renewed the show for a 4th season and greenlight Equestria Girls. So you could see why Magical Mystery Cure is the way it was.
Even though I'm not a big fan of Alicorn Twilight at all, I could see why Hasbro would do it in order to continue the show, even if the idea comes off as corporate shilling.
Equestria Girls: That was also a situation of bad timing and corporate driven. Not to long after the Twilicorn fiasco, Hasbro announced Equestria Girls. Everyone is upset about it because it feels like Hasbro was trying to cashing in Monster High. While it's true that fans blow this whole thing way out of proportion, but at the same time I kinda don't blame them because the idea of having candy colored horses turned into high school girls and place them in a generic high school setting was a major turn off.
Although, nowadays, a lot of people don't hate Equestria Girls anymore after Rainbow Rocks came out.
Personally, I wasn't to crazy about Equestria Girls all that much, but at least I'll say it somewhat better than later seasons of FiM, but that's not saying much.
I could go on, but I don't wanna talk about it anymore.