These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
All Adult Animation Is South Park: Averted. He was around long before South Park was even a gleam in the eyes of their creators (he nearly sued them because their character of Mr. Hankey was too similar to an idea he'd tried to pitch) and, despite his juvenile, off-the-wall humor, hasn't had quite as much vulgarity in his work as many would expect him to... that is until the Ren and Stimpy: Adult Party Cartoon came along and he was pushed to do wall-to-wall vulgarity to compete with the rising popularity of South Park.
This, generally, is an attitude he does his best to subvert - while he enjoys classic Disney works for being slick and well produced, he's far more partial to Warner Bros. and other companies for their rawer, more anarchic style.
Base Breaker: A lot of his more recent cartoons, but notably Adult Party Cartoon. Fans weren't impressed by seeing figures from the childhood in such an adult cartoon, even for characters as subversive as Ren and Stimpy.
Broken Base: Fans of Ren and Stimpy that aren't impressed by his adult cartoons, versus fans that don't mind.
Never Live It Down: He has deeply regretted some of the decisions he made in his works, such as his use eyes that squish in the middle to form a ) shape (which he only meant for the storyboards and never actually wanted them in the final cartoons) as well as many of the mistakes he made in his cartoons, such as one scene of Stimpy's eyes defying proper perspective (which was a sloppy mistake, but "everyone thought it was on purpose") and claiming that many TV cartoons (such as Animaniacs) had made "whole styles out of his mistakes."
In fact, he encourages fans *not* to study his work, and instead look at his influences for education, such as Bob Clampett.
Scapegoat Creator: He is largely blamed for the failure of Ren and Stimpy: AdultPartyCartoon, with fans claiming that he got too much creative freedom on the latter which "ruined" the show—even though John has pointed out that the show still went through Executive Meddling and censorship (this time, through Spike TV instead of Nickelodeon, though both channels are owned by Viacom, so it's really a case of "same shit, different dump"), forcing him to put in excessive adult humor to compete with South Park (though, at the time, South Park was at that point where it was mixing in social commentary with its gross-out humor and taking it beyond fart jokes from the 1990s) and [adult swim] (which doesn't really delve in gross-out humor. [adult swim]'s humor is laden with pop culture references, Dead Baby Comedy, and/or bizarre, non sequitur humor).