Hey, welcome to the boards, OniWolf! This is a really amazing first post. Many 20-minute or longer reviews of the film (or any film, for that matter) seem to end up rambling barely five minutes in, so I think you really accomplished something with your take. You said all that needed to be said and more.

I'll get in some comments, though I won't cover everything. I'm sure others will have more to say.
I would argue that the original games, despite their whimsy, were
already pretty dark. Not necessarily in tone, of course, but definitely in concept. Mario and Luigi regularly massacre hundreds, if not more, of Koopa's army. Yoshi himself eats just about anything, including Koopa's aforementioned army that is clearly of human-level intelligence. (It always bothers me as a mammal and an ape to have Yoshi eat and digest into eggs the monkeys in Yoshi's Island

)
I agree that Leguizamo's Luigi is often inconsistent in tone, though I also feel that his character is one of the best in the entire movie. He put his all in that role and really gave us a memorable Luigi, especially considering the official characterization that would come from Nintendo in later years.
Hopper's Koopa, however, is more disappointing in his tonal inconsistency. He's such a brilliant actor, especially in his villains, so you would have hoped for a better performance from him.
I'm glad that you were able to identify all the references in the film to the source material, especially the police chase scene and how it relates to Super Mario Kart. Many people don't catch that. The funny thing is that in the earliest version of the script Koopa actually held a "golf tournament of doom," which was obviously inspired by the original Mario Golf.
Finishing up, that artwork is the coolest thing ever! That was the best way to end this review.

I particularly like how you drew the reptilian Koopa. Still "human," overall, but with some creepy reptile traits. If you're interested, we'd be happy to showcase the piece on our site under the Fan Art section.