Actually, That's My Assistant: When Lisa first sneaks into the boy's school, he finds that Principal Skinner has been demoted to Groundskeeper, before Willie walks over and points out how Skinner is Assistant Groundskeeper.
Be Careful What You Wish For: After Skinner's little slip up about girls and math, the one thing principal Upfoot spends money on for the boys side of the school is a math teacher that teaches 7th grade math far beyond their current level. After sneaking in Lisa loves this, as it means shes actually being challenged to learn rather than to talk about her feelings.
Epic Fail: Assistant Groundskeeper Skinner's attempt to poison the squirrels infesting Springfield Elementary.
Principal Upfoot's attempts to teach the girls math were treated as more of an empowerment seminar....and as Lisa pointed out didn't actually teach them anything about math.
Fridge Horror: Nelson never finds out that the "boy" he had beaten up in school was actually Lisa Simpson, whom he had dated and had feelings for. Imagine the guilt he would likely experience for a long time had he found out.
Godwin's Law: During the diversity forum, Skinner gets called "a worse version of Hitler" by an audience member.
Hypocrite: Melanie Upfoot for all her attitude towards Skinner was appropriate given his sexist remarks, was a misandrist. She divided up the school by gender, took what little funding the school had and used it exclusively to improve the girls side while the boys side had turned into a ghetto
Jerkass Has a Point: While what Skinner said was sexist, the way the girl's school was taught wouldn't really give them any knowledge as why Lisa sneaked in the boy's school because it was regular knowledge.
Political Correctness Gone Mad: What Skinner said was definitely reprehensible but segregating the entire school by sex is disproportionate. Both sides suffered from this, the boys were treated like animals while the girls were denied proper education.