It probably should never have happened. Matt Groening was so disgusted he had his credit removed from the episode!
Well, it wasn't so much that it was bad, but I think the Critic crossover was something that was foisted upon the show by Fox, and he was unimpressed by being co-opted into its marketing.
However, it is one of my least favourite episodes, not for that reason but because it's a really terrible plot and story. It's all based around Barney making a film about alcoholism and Homer being pressurised to choose it as the best in the Springfield Film Festival he's judging, but a) who cares if it wins, it still got made, b) Barney has never before or since shown any kind of self-awareness about his alcoholism (I know he later got sober, but the point remains) and c) in every other episode everyone hates Barney apart from his mate Homer, and now suddenly everyone loves him and Homer's the bad guy! Useless episode.
The Critic's creators had previously been Simpsons showrunners, Bart's VA Nancy Cartwright was one of the main cast members and a few other voice actors also worked on both shows. That created a misconception among the public that Matt Groening had created The Critic (Futurama didn't exist yet to prove he always uses a specific art style), so he did his best to make sure his name was disassociated with it.