These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Dark Horse: Just like his original short, the Mad Doctor (or rather, Dr. XXX in the original short) is remembered quite fondly in particular. Helped out by the fact that the cartoon and character is by far and large the most obscure cartoon in the game.
Genius Programming: The Sega Genesis version of the game features Mode 7-style perspective effects in a number of the levels... produced entirely in software, as unlike the SNES, that system has no hardware support for such effects. In fact, the SNES version even lacks one of these levels.
Right before the boss fight against the Mad Doctor begins, he removes a black cloak that makes him resemble the Phantom Blot, Mickey's lesser-known archnemesis from the Mickey Mouse Comic Universe. The Epic Mickey game would later feature the Mad Doctor and a revamped version of the Phantom Blot called the Shadow Blot as the main antagonists.
Most Annoying Sound: When Mickey is hit, he will say either "Ow!" or "Uh-oh!". Considering how difficult the game is, these phrases quickly become very annoying, especially the latter.
Narm: In the Playstation version of the game, Mickey will for some reason always enter an animation that has him checking his watch when he finds Pluto at the end of the Mad Doctor stage, making him seem completely uninterested in having found his pet.
They Wasted a Perfectly Good Plot: A minor example. It's a great game and a good 65th anniversary tribute to Mickey, but one wonders why there was no level devoted to the "Sorcerer's Apprentice" from Fantasia. That's one of Mickey's most iconic moments.
Perhaps because that was a segment from a Disney Animated Canon compilation film and not a proper standalone Mickey Mouse short.
That and there was already a game featuring the Sorcerer's Apprentice aka the Fantasia Genesis game.