This is a rough episode of television. In general I'm finding the New Scooby-Doo Movies not to be that great; this one has got to be one of the worse ones, but also really highlights some of the general flaws of the New Movies. In no particular order:
The Stooges were not particularly funny - it's possible I just don't "get" the Stooges, my parents were Marx Brothers fans so I never saw any of their movies growing up - but I suspect this is a particularly weak turn for them. In their defense, at least everyone still knows who the Three Stooges are, unlike episode 4's Jonathan Winters.
A broader problem with the way they do guest stars is that so much time is devoted to introducing and giving laugh lines to the guests, that we don't really get a good introduction to the eventual villains. Not like the villains had a ton of depth in the original show, but the big reveal is less fun in the New Movies because more time had to be spent on the guests at the expense of the bad guys.
The writers seem to have struggled to spin the original Scooby-Doo format out from 23 to 45 minutes. The original series generally has really tight pacing, starting with a tease of the monster, then a series of spooky encounters and clues, leading up to a big reveal. Here, they try and do a mid-act mini-reveal of some sort but it never really lands.
This episode in particular (or at least the copy that's available on Boomerang) has several glaring continuity errors in the middle that make it difficult to follow. It seems like Velma's Act 2 disappearance was shuffled late in production - she disappears, then everyone goes to search for her, but for one quick shot she's back with the group. Later when Shaggy and Scooby are rescuing everyone, they say they're rescuing Velma, but at that point they already know that she's been reunited with Fred, Daphne, and the Stooges.
There's also some plot points that are just really bizarre! I wasn't able to follow what the backstory of the massive, extraordinarily sophisticated dinosaur vehicle was, or why the bad guys had a literal bat mobile.
The show definitely still has its moments, and the performances from the series regulars is great as always. Shaggy and Scooby are hilarious, and the whole gang are great characters that you really do enjoy watching look for clues. Unfortunately, this episode's flaws mostly drag down the fun parts.