Why was the Captain Underpants personality so dangerously stupid? The hypnosis would have been limited to Krupp's understanding of the superhero, whom he hated at the time. The stupidity was something of a subconscious mockery.
On the other hand: The first time he goes in their treehouse, Captain Underpants comments that it contains mementos from his many adventures. How would Krupp know this? He read the comics!
This theory also works for the books: In the fifth book, Mr. Krupp read a comic George and Harold where wrote that Captain Underpants was temporary defeated by spray starch and when he was later sprayed with spray starch after turning into Captain Underpants, he thought that he lost his powers until George and Harold wrote a comic book that said that he was "immune" to spray starch.
Melvin admitting to telling on George and Harold is more than just smug bragging on his part—he's such a tattling little toad, he can't even help telling on himself.
If we take it that Captain Underpants is in part an unconscious reflection of Krupp's good side that's been buried under years of bitter loneliness, then it makes total sense that he found their comics Actually Pretty Funny in the end. He might have always been able to enjoy that kind of stuff but just was never in the mood to give it a chance before.
When Professor Poopypants is checking to see if Melvin has a sense of humor, he shows him a series of humorous clips which he (in spite of his goals) finds funny. One clip he says is "really good" shows a man about to slip on a banana peel but is hit with a safe instead. Naturally you'd assume that this can be chalked up to classic schadenfreude, but on further analysis, that clip showed a typical comedic scenario (slipping on a banana peel) and subverted it (being hit with a safe instead.) In other words, it's an anti-joke. A pretty fitting thing for the humor-hating Poopypants to enjoy.
Given he is Principal Krupp's Shadow Archetype (somebody eviler than him), it's possible that Krupp is friendless and lonely in his adult life because kids used to make fun of his last name, too.
There's a reason Harold likes dolphins: they're basically just like himself and George in personality. They're smart, friendly, playful, mischievous, and their animal call sounds like laughter.
Mr. Krupp has been proven to be petty and a fan of Disproportionate Retribution—he gleefully tells the boys he is going to "annihilate [their] friendship" instead of just separating them, and he rips their comic book to shreds rather than just taking it away. He even fired a teacher for wanting to skip the Invention Convention and spend time with his family... which, we learn later in the film, Krupp does not have. It wasn't just retribution for not attending a mandatory event—Krupp was most likely jealous, and overreacted accordingly.
As a kid, this movie is hilarious. As an adult, the idea that you have an uncontrollable split personality controlled by two ten year olds and you have no idea how it's triggered or that it even exists, all you know is that you're having blackouts and then ending up in really crazy situations half-naked, soaking wet and with possible unexplained injuries...to be fair, it could be a lot worse if George and Harold weren't decent kids who don't want to see Krupp get hurt despite what he's done to them, but if they weren't, it could be a very bad situation.
It's a good thing the shrink-ray wasn't set to large-ify when it hit the school. Considering how big Poopypants became when he was hit with it, it's very likely that a giant falling school would crush and wipe out the rest of the city.
Even before Professor Poopypants' plan, this school was essentially brainwashing kids to be unimaginative and miserable, and the parents (likely) had no idea!
According to Professor Poopypants, Melvin Sneedly is physically incapable of being able to laugh at anything. Go on, think about that for a minute.
Harold destroys Poopypants' shrink/enlarge ray after the professor is shrunken down to insect size. While Poopypants is likely smart enough to figure a way how to restore himself to normal what about the giant blue bird, the shrunken passerby, and everything else that was hit with the ray when it went haywire during the climax?