The scenes that most people remember are Bart skateboarding naked and Homer having Spider-Pig, each of which happen before the main plot (Springfield having a dome put over it, due to being environmentally unsafe, and the Simpsons escape, due to the residents wanting to execute them after Homer caused it).
Back when the movie was released, it was amongst the highest-grossing movies, so its not like it was some niche movie.
I only saw it once in theaters and I sorta checked out about 2/3rds of the way through. I suffer from "comedy fatigue" and I prefer my comedy material to be shorter, like an hour tops.
I agree with this very hard.