Dawson Casting - Veronica is implied to be 17 years old at the beginning of the show. Kristen Bell was 24 when they shot the pilot. Also Teddy Dunn (Duncan) and Jason Dohring (Logan) are a couple of years older than their respective characters.
The unreleased season 4 pitch features in In-Universe example: Veronica now working for the FBI goes undercover as at a girl's reform school to catch a warden who is molesting the students
Also, according to the actor playing Wallace, UPN made it clear to Rob Thomas during season one that they would never allow him to pair Wallace and Veronica up romantically, due to the network thinking no one would watch a show where the main character (who was white) was dating a black man.
Real-Life Relative: Married-in-real-life Harry Hamlin and Lisa Rinna play Aaron Echolls. Wallace's little brother who appears in a couple of episodes is played by Percy Daggs' real brother.
What Could Have Been - Meg Manning's death: She was supposed to have died in the bus crash, but UPN demanded at least one survivor due to them not wanting to open the show's second season with a bunch of dead teenagers. So Meg (who was supposed to die) lingered in a coma with the plan being that Meg's mother would euthanise her possibly braindead daughter and Veronica (hiding in the room) would witness this and be busted by hospital staff members, after Meg was smothered to death when she comes out of hiding and removes the pillow from Meg's face. This got shot down too (though Thomas was allowed to film it as part of a stunt "alternate ending" that was posted on the show's UPN website). So instead, the episode that aired ended instead with the reveal that Meg was pregnant with Duncan's baby and her waking up just in time to give birth and die from a brain hemorage.
Similarly, Dick was supposed to be a suspect for the Hearst Rapist storyline and Rob Thomas even admitted that they had a retcon in mind to establish Dick secretly being on campus during the season two episode that started the arc, this was abandoned.
Season Four was supposed to have been a complete reformatting, complete with time skip and firing all cast members save for Kristen Bell. The relaunch would make Veronica a FBI agent, going on undercover assignments with a new milquetoast boyfriend agent and actor Walt Goggins as her supervisor/mentor.