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.
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I think the big issues with the movie is that it is not particularly long (Wikipedia says it is one hour and 27 minutes long), the actual plot does not start for a while into the movie and it does not have an "epic" feel to it (unlike South Park: Bigger, Longer & Uncut). It really is like an extended episode or multi-part serial.
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