I think my only gripes with the movie were about two things.
One was how there was actually some of the IRL music usage despite how the trailers seemed to stay completely away from that. It felt a bit jarring at first when the first one is during the penguins charging before it cuts out, and I think the "Take on me" usage felt kind of out of place in particular and could have done with a game-inspired song there, but maybe that's just whiplash from something that was subverted by the trailers being double subverted in the film proper (and it could have been worse when I remember crap like the greentext thinking it'd be "trashy 3D kids movie but with Mario"). Then again, I didn't mind the Uptown Funk part of Sonic 2, but somehow that felt less unexpected. I will say the Mr. Blue sky usage at the end was fine. Looking back now, I can at least appreciate they kept it to a minimum.
The other things were a few things that were underutilized, namely Foreman Spike and how we don't see what the Bros.' life was like when they still worked for him. There was also how where Peach came from is left up in the air, but if the Sonic movies are anything to go off of, this one especially sounds like something that could be explained in a sequel, which they already seem to have ideas for if THE Yoshi is already planned to appear based on that post credits scene.
Anyways, as for good things, overall it was still a very fun and enjoyable movie with a lot of heart put into it that doubles as a love letter to the series, and I even enjoyed several of the comedy bits. As for a particular highlights, I think they did good portraying Bowser's serious and goofy side (and some good laughs were had in those parts too). I also wasn't expecting the final battle to take place in Brooklyn, and it was cool to see how Luigi still factored into it despite spending most of the movie captured by Bowser. I also got caught up in trying to catch little details in parts of the movie, so it's definitely rewatch material.
On the subject of those details, seeing that other classic games like Kid Icarus and Star Fox exist in the Mario world, I wonder who's the face of Nintendo in that world, especially when Balloon Fight and Punch Out seem to not be games with the pizzeria and a billboard respectively.
Lastly, I was touched to see Satoru Iwata's name in the credits. It's been years since I saw his name in a credits sequence since all last games he worked on have since come out, Seems like this and Super Nintendo World are the last things he worked on to come out of the woodworks.
In short, If you're a Mario fan, I guarantee you'll love the movie.