Broken Base: The series as a whole. Is it too similar to the original? Fans of the late 90s, early 2000s direct-to-video films such as "Zombie Island" and "Cyber Chase" often complain the reboot is too strict to formula and generally not as fun (or well animated). Fans of the original pre-Scrappy cartoons may complain that it's too "modern" and "realistic" compared to the older shows, along with over-lampshading the old formula and not being as scary.
Fandom Rivalry: With Scooby-Doo! Mystery Incorporated. They're two popular, early 2000s modernizations of the series on two polar sides: "What's New" keeps things mostly traditional and more true to real life, while "Mystery Inc" vastly reworks the personalities, designs, and general series. Obviously the debate mostly revolves around the former being bland and boring or the latter ruining the characters (especially Velma and Fred).
Fridge Brilliance: In Fright House of a Lighthouse, the Creepy Keeper is attracted to Scooby in his mermaid disguise, which doesn't seem to make sense when the ghost turns out to be the female Verona Dempsey. Then you realize that it's a joke - Verona is an Expy of Velma, and it's long been rumored that Velma is a lesbian.
Hilarious in Hindsight: In the teaser of "Toy Scary Boo", the "living" Spaceman Swinton dolls build a long ladder out of building bricks resembling LEGO, which now have Scooby-Doo sets.
They Changed It, Now It Sucks: While some people praise the show and hail it as a return to "the good old days," this show has received criticism, mostly from those who preferred the older 1970s series, due to changing the character designs and animation, music and sound effects, trying to make it more "hip" and "current," among a few other things.
It's the Same, Now It Sucks: To some, the return to the previous formula was fine, but it's the fact that the only thing that was different was the overt lampshade hanging and certain mannerisms of the gang. It was regarded nice returning to the formula, but doing little variation with it was something of a major problem for some.
Ugly Cute: The bat that Shaggy and Scooby thought was Fred in "The Vampire Strikes Back".