I have to admit I enjoyed this episode more than any in recent memory. We've had a long string of insufferable episodes, but this one was totally sufferable. Notably, there were strong plot problems, especially towards the end.
First of all, Homer's attitude towards Bart's schoolwork is unbelievably out-of-character for him. And sticking to his guns when Marge tried to get him to lighten up? For Duff or doughnuts, maybe (even then he's typically a bit spineless) but to make Bart do homework? What?
Later on, Homer and Marge were supposed to be stopping Bart in order to save their marriage, yet when the two reached the hidden subway entrance, Marge disappeared and it was all Homer. The same Homer who was the one that wanted Bart under control throughout the entire episode. So where did Marge go? Did she have second thoughts? Could she not keep pace with her morbidly obese husband? How does either possibility make any sense? Shouldn't they have stopped Bart as a team? Sure, it's cliche, but so was this whole episode. At the very least, if they're not going to use the cliched ending, they need to explain why they're not doing so, and hopefully make it funny. The Simpsons used to excel at this.
Secondly, right after Homer throws the kill switch and the ground stops shaking, Skinner exclaims, "the school is saved!" Really, Skinner? Despite the fact that you have no idea what is causing the tremors? Despite the fact that you, as a man of at least grade-school science knowledge should be able to ascertain, the tremors have been occurring semi-regularly and you have absolutely no reason to believe that that was the very last one? Unless the reason Marge disappeared is so she could call Principal Skinner and let him know of Bart's plan... yes, that half-assed explanation will do nicely.