It really is a great series, unfortunately overlooked by most people who weren’t previously all that enthusiastic about Scooby Doo, which is a lot of people.
And even those ridiculously contrived villain plots are explained. Everything is! Every question anyone ever had about why all these bad guys dress up as monsters, why nobody seems to care much that a dog can talk, why Fred always devised Rube Goldberg traps, even why there are multiple cartoons about small groups of teenagers solving mysteries with animal sidekicks….all spun together with the same outlandish, even reasonably creepy Lovecraftian backstory.
There are shades of Stephen King’s IT, especially in the aspects you just mentioned. Character writing nobody probably ever expected from Scooby Doo. The writers even seemed to do their best to kind of have a same-sex relationship in there, though like most cartoons on network TV with an all-ages audience, they wouldn’t have been allowed to be overt with it.
And then there’s the demented parakeet with an army of thinly-veiled-nazi robots.