Captain Obvious Reveal: Alicia Silverstone's character Heather Jasper-Howe being the Big Bad. You have to admit, a famous celebrity playing a supporting character in a Scooby-Doo movie would definitely tip a few people off.
Fanon Discontinuity: Inverted. The first movie was pretty much not mentioned at all in the second film, which made hardcore fans extremely happy.
It Was His Sled: Jonathan Jacobo is still alive and IS Heather-Jasper Howe.
Ham and Cheese: Tim Blake Nelson as Jonathan Jacobo, Peter Boyle as Old Man Wickles, and Alicia Silverstone as Heather Jasper Howe ham it up to the best of their abilities, and are clearly having a blast doing it.
So Bad, It's Good: While the film isn't exactly Oscar bait, a lot of people enjoyed some of the genuinely good attempts at praising the Scooby-Doo lore and capturing some qualities from the classic cartoon.
Realistically, this might be the best way to take the film by nonfans, or people older than kid age. It's been pointed out in places, most recently by the Nostalgia Critic, that the film actually has a decent amount of comedic potential, it's just that the actors didn't have the comedic potential to make it all work that well, or maybe got poor direction, despite the fact that James Gunn wrote the script.
Surprisingly Improved Sequel: For those who hated the first movie for not following the cartoon close enough, this sequel rectifies this. Critics didn't seem to think the same, however, as this movie received even worse critical reception than its predecessor.
Great idea, Daphne. Try to beat a ghost made of living electricity by kicking it. Obviously didn't take 6th grade science.
Shaggy and Scooby accidentally create more monsters while randomly screwing around with a machine they know nothing about. Granted, they didn't know it made monsters, but they've done this song and dance enough to know better than to mess with sort of stuff now.