The biggest part of what was going on, of course, was that Ghostbusters had just come out and Hanna-Barbera decided to re-tool its most re-tooled franchise yet again. So there were not only real ghosts and monsters (they'd been doing that for several years anyway), there was a "Vacu-spook" to suck in the spooky ghosts, and there were two comic-relief ghosts both of whom were actually more annoying than the cartoon version of Slimer. All this might have been just an extension of what H-B had done already. But the show also added a ton of new characters. Freddy and Velma had already been dropped in earlier incarnations, and they didn't appear here either, but in addition to Scrappy there was a wise-ass human kid, "Flim-Flam," who was like a human version of Scrappy, and Vincent Price voicing the ghost expert and wizard "Vincent Van Ghoul," and then there were the two very poorly-drawn ghosts voiced by the old-school comedy pros Howard Morris and Arte Johnson, and... well, I'll let Tom Ruegger, the associate producer and story editor, tell it:
Now, who I really couldn't stand was Flim Flam (from "The 13 Ghosts of Scooby Doo.") Definitely the product of network focus groups: "We need to get a kid in there." Flim Flam never worked out. Total drain. We carried a lot of character baggage on that show. Vincent Van Ghoul. Bogle and Weerd. 13 ghosts. Live and learn. After that version of the series, the only thing to do was start over. Which is what we did with "A Pup Named Scooby Doo."
The producer was Mitch Schauer, a fine director and producer who later went on to do Freakazoid! and create Angry Beavers. He would later joke that he was "The Man Who Killed Scooby-Doo." He came up with some decent design ideas in what appeared to be the first attempt to make a genuinely scary Scooby-Doo show, and occasionally it looked better than H-B average, but the animation was of course bad (Virgil Ross is credited as one of the animators on the series, and I bet I could identify his scenes if I looked hard enough, but I don't want to look that hard), and the look of the whole thing was like the apotheosis of the ugly, flesh-colored-eyes look that H-B and Ruby-Spears had been foisting upon us for a decade. Not a pleasant show to behold.
The scripts weren't much, either, as you can imagine, though they did -- and here's the part that still intrigues me a little -- keep sneaking in the occasional joke or scene that wasn't in the traditional H-B house style. I guess that's what confused me as a kid, along with all the bad new characters. None of these jokes were enough to make the episodes good, mind you; they were just little things that the writers were throwing in for their own amusement. In the weirdest moment, which I still remember after all these years, the episode breaks for a "Special Report" where Scrappy interviews a parents' advocacy type who's concerned about the violent use of fire in the episode, which involves a dragon. Scrappy accuses her of being prejudiced against dragons, Scooby and Scrappy reduce her to tears at her insensitivity toward dragons, and we cut back to the episode as if nothing had happened. That, for better or worse, is the ancestor of the whole self-referential style that was all over TV cartoons in the '90s, and sort of shows what I meant when I used to say that Tiny Toons was the culimnation of something many of these writers had been trying to do at H-B for years.
None of this is meant as a defense of 13 Ghosts, the show that even Deputy Dusty fans couldn't quite swallow. But for students of TV animation history, it's kind of interesting to see the seeds of what would happen on better shows. A similar case is another H-B retool from the same period, The Super Powers Team: Galactic Guardians, where writers and producers including Alan Burnett overhauled the Super Friends into something that pointed toward the '90s Batman cartoon. (Though Galactic Guardians, unlike 13 Ghosts, was a pretty good series on its own terms.)
The "Special Editorial" occurs toward the end of this YouTube clip, at about 8:30.