These videos are often criticized because of their poor quality, as characters speak in subtitles almost exclusively, the plots often make no sense, and they tend to have so many characters that none have effectively established any personality. Some characters are taken way out of character for the sake of the plot.
They have also been the subject of slander by various users on sites like YouTube, DeviantArt, and even Tumblr! The series gained a lot of notoriety when noticed by users like BlackBusterCritic, who is not well-liked by many crossover fans, due to his comedic shenanigans against their community.
The fanbase is arguably the worst of the entire thing, due to a lot of users being unable to take even the slightest bit of constructive criticism, and painting anyone who does criticize them as a villain. This was one of many things that even led to long-time contributor BennyTheBeast discontinuing such projects.
Some character alliances could also be called into question, for example; Twilight Sparkle's romantic relationship with Thomas the Tank Engine, which became an infamous OTP.