A) The mysteries were almost all immediatley solvable (sometimes they even show who the villain is behind the mask!)
B) The animation quality... well... it's a lot more... rubbery. That's the best way I can describe it. You'll notice it in some of the worse episodes, where the artwork is downright lazy. Though each guest star bore a good likeness to his real life self, the animation quality was definatley inferior, possibly due to the length of each episode.
C) The comedy! I'm not objecting to the comedy, because that's the filler in between the mystery and chase bits, but 85% comedy, 10% mystery, and 2% plot? I think they pushed this one too far. But then again, what else do they need the guest stars for?
Overall, the Scooby Doo Movies weren't all bad. Some episodes were truly memorable (Don Knotts, Don Adams), while others were terrible (Batman, anything else with another cartoon gang in it).