This movie's version of Luigi acts a lot as if Wario was on Mario's side. Interestingly, this is the only time Luigi doesn't wear green.
All the Toads are female, at least those who were rescued.
Unlike other variations of Bowser, this one is clearly a Stalker With a Crush with a very kind and almost innocent personality.
Ass Pull: The reveal that Kibidango is actually Peach's fiancé, Prince Haru.
Broken Base: The ending. Some people don't mind that Peach was already engaged to Prince Haru, finding it to be a clever (if abrupt) subversion of the common gets the girl in the end trope. Others were absolutely furious since Mario went through all that trouble and the revelation came out of nowhere, as well as Mario/Peach being near-canon in the games.
The scene where Luigi and Mario getting out of the cave. Immediately after Luigi squeezes out of the hole he dug, he runs back in the cave, which is sealed by a wooden gate, and tries to hide from the Hammer Brother By running through the gate and breaking it.
Die for Our Ship: Going by YouTube comments, Prince Haru comes under fire a lot for marrying Peach instead of Mario.
Ear Worm: The song that plays over the opening credits.
In Mario's fight with Bowser, at one point, he grabs Bowser by the tail and throws him away. Guess what you have to do in Bowser's boss battles in Super Mario 64. Additionally, one scene in the film also involves Mario entering a sunken ship, just like in Super Mario World.
This film used the idea that Bowser is in love with Peach years before Paper Mario 64 and Super Paper Mario practically made it canon. What's more, a plot with Bowser kidnapping Peach with intent to marry would later be canon in the games, and like in the movie, she doesn't marry Bowser or Mario, though for much different reasons.
Luigi in this film wears yellow and is obsessed with money, just like the later character Wario.
Bowser, a character who we now associate with Kenny James' badass Guttural Growler voice and an Expy of the Ox King, is here voiced by Akiko Wada, famous Japanese female rhythm-and-blues singer.
Peach is voiced by then-popular J-pop singer Mami Yamase. The fact that she's an idol and not an actress is apparent, and not helping is that she makes the seemingly adult princess sound like a petulant, nasally ten year old.