I too think The Principal and the Pauper is a good episode. While it’s usually described as a “shark jumper” I think that’s the entire point of the episode-- how weird can we get with this show? Unlike the episode of Happy Days where Fonzie actually jumped a shark on his motorcycle waterskis (thus providing a name for the concept) and it was supposed to be serious, The Principle and the Pauper knows it’s jumping the shark and has fun with it.
There were multiple times when The Simpsons made minor allusions to the self-referential “this is a cartoon, it’s not reality” idea, but The Principle and the Pauper took it to a level some viewers didn’t like. I’m actually more disappointed that in a later episode they mention Armin Tamzarian again, despite Judge Snyder’s verdict that nobody mention him ever again “under penalty of torture.”