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I honestly feel like the first movie got everything right that the second got wrong, and vice versa.
>First makes Plankton too menacing, second makes him too goofy
>First was very cohesive, second movie felt like a bunch of different plots
>First didn't focus on Sandy enough and it felt like some main characters became minor, second has better balance on characters, but it feels like Patrick isn't present enough after his role in the first movie
>First had a darker tone that felt similar to the later seasons, second was made to be lighter and the characterization/references made it feel closer to earlier seasons
>Both have Bikini Bottom collapsing into ruin and scenes above water, but play them completely differently: first movie has it under a dictatorship and Spongebob is powerless above water, second has it in anarchy and Spongebob is superpowered above water
>First is full of thugs and monsters, second has a goofier villain
Even the artstyle reflects this: the first has more subdued colours, grosely-detailed monsters, and the moment where Spongebob has a five-o-clock shadow; the second is brighter and softer, even in the apocalyptic scenes.