Not an omission, but I'd combine the Fleischer shorts (Betty Boop, Felix the Cat, Popeye, etc.) into a single entry for the same reason as the Looney Tunes and Disney ones.
The Fleischer's had nothing to do with Felix the Cat.
I wouldn't object to combining all the Fleischer studios cartoons except for the fact that Popeye, Superman and Screen Songs were eventually handed over to Famous Studios so if you were to just lump everything together based on the studio you would have to divide some series between the different studios that handled them over the years.
16 should explicitly be "Scooby-Doo, Where Are You?!" All other Scooby-Doo shows derive from it, and it's the original with the classic "It was really X all along!" setup.
Well by your previous logic what's wrong with lumping it all together? Scooby Doo is a pretty big franchise.
Other than that, I'd recommend dropping "Hong Kong Phooey", "Top Cat", and "Wacky Races". I don't see them being on the list for any reason other than being old Hanna-Barbera cartoons. Switch them with Adventure Time, Archer, and My Little Pony: Friendship is Magic. The sheer cult following of MLP and its huge popularity across multiple demographics should give it a Top 100 spot. Same with Adventure Time.
Yeah and now I already hate you.
Regardless of how you feel about their quality a lot of Hanna-Barbera cartoons have lasting popularity, especially Wacky Races which is still heavily recognised in American popular culture despite being a show that lasted 17 episodes, pretty impressive I say.
Friendship is Magic should never be on this list. I don't give a fuck how popular or acclaimed it is, I don't give a fuck if revisionists 50 years from now hail it as a masterpiece. Fuck that cartoon, fuck everyone who likes it, I'm biased.