Designated Villain: Krudsky is treated like crap by both the gang and Fairy Princess Willow even before he does anything villainous. In fact, it's this that motivates his evil plot in the first place. Yes, he was a Jerk Ass, but even so...
Apparently he was treated like crap all his career, and Scooby and Shaggy's payback was the last straw. Making him a Jerkass Woobie.
Is this a direct joke by simply having Scrappy dolls ran over being a Take That! against Scrappy?
Is it the fact that it was the mystery machine being hijacked by evil that does it a Take That! against fans who would have to be monsters to attack Scrappy?
Or is it just a gag that people are only thinking of as a Take That! because it's The Scrappy. Given What's New, Scooby-Doo? had the Roller Ghoster crash into dolls of other Hanna Barbera characters several years ago, and this movie clearly being inspired by Scrappy-era movies was a Shout-Out with nothing more intended.
Unintentionally Sympathetic: Krudsky may be a jerk himself and doesn't even think twice about causing havoc with his new power, but him being treated like a joke for his entire career, having his act ruined and getting put out of a job by Shaggy and Scooby solely because he doesn't allow dogs, and getting harassed by Fairy Princess Willow without even doing anything to her, it's hard to not feel a little bad for him. Heck, you might even end up wanting to take his side!