Originally "This is your school" was different.
You were supposed to get Bucky's One-Eyed Elf Statue back, possibly instead of Eunice's chocolates. Someone posted earlier that originally Bucky was the kissable Nerd, perhaps he was supposed to be the first kiss in the game instead of Eunice?
Also, Gary originally talked Jimmy through school rules in this mission, and the cutscene where he talks about all the cliques was originally not meant to be a cutscene, but rather happen during gameplay.
In Complete Mayhem, once the clique leaders were defeated, they were originally going to have a small conversation with Jimmy about getting their clique back in order. Also, Gary originally had many more lines he could say over the speaker, 10 in the audio files. Petey was also meant to appear in this mission, in the audio files he has a few lines for it. And speaking of Petey, like Gary he has lines for dodgeball games.
Also, both Complete Mayhem and Final Showdown are listed as being part of Chapter 6. Chapter 5 could have possibly ended after "Showdown at the Plant".
Firecrackers were going to be called Cherry Bombs.
The girls have dialogue recorded for being given a swirlie, implying you could originally grapple them.
Gloria was originally going to be older, well either that or Jimmy was able to kiss the younger girls, as she has dialogue recorded for being given a gift and being kissed. If she is made kissable with mods, she will use these lines.
Everyone has dialogue recorded for being given gifts, implying you could originally give things to anybody. Everyone also has dialogue for tattling, showing that originally more than just Little Kids and Const would do this.