- Executive Meddling: In the very early stages of development, the game's designers gave serious consideration to scrapping the stage select and replacing it either with an entirely linear level structure, or something akin to the map system from the then-recent Super Mario Bros. 3. Capcom overruled them, though later games in the series would experiment with the level structure a little more.
- Magnum Opus Dissonance: Inverted; while the game is Keiji Inafune's least favorite entry from the Classic series — albeit not the one he considers the worst, with that title going to the Game Boy Mega Man II — a not-insignificant number of fans consider it to be the best game in the whole Mega Man franchise.
- Name's the Same: Gemini Man is not to be confused with an upcoming action movie featuring Will Smith.
- Troubled Production: The lead planner behind Mega Man and Mega Man 2, Akira Kitamura, left Capcom while 3 was in the planning stages, forcing Capcom to assign talented programmer Masahiko Kurokawa (who had already made a name for himself on other Capcom projects, but hadn't worked on a Mega Man game before) to the team. According to this report, Kurokawa didn't mesh well with the new team (particularly Keiji Inafune) and abruptly left the project halfway through. This lead to Inafune having to step up and pull together a completed game in a very short time — with his own lack of experience at being the lead designer of a game in turn forcing him to draft in DuckTales designer Yoshinori Takenaka for assistance — leading to a number of technical problems and cut content.
- What Could Have Been: As detailed in Obvious Beta on the main page, the game was released unfinished due to a rushed development schedule.
- According to Keiji Inafune, all eight stages were originally planned to be revisited for the Doc Robot portion of the gamenote , Break Man was supposed to be a totally unique boss (instead of being a reskinned Proto Man), and the Skull Fortress was supposed to be much more expansive (evidenced in the "map screen" transitions; this is the only game in the Classic series where the map and the actual level layouts don't match, with the map believed to show the intended stage layouts), among other things. All this wasted content is the main reason why Mega Man 3 is Inafune's least favorite game in the Classic series.
- The original plan for the game was for the Break Man fights to have a logical progression, with story moments before and after each fight. Unfortunately, the rushed development and the implementation of stage select (which prevented the development team from being able to easily say that, for example, the encounter on Gemini Man's stage would happen first to set everything up) made it impossible to add. Instead, the Break Man battles are just seemingly random attacks from a red robot, and the encounter on Gemini Man's stage is just confusing.
- As revealed in the Complete Works book, the original concept for Top Man's stage was lost when someone accidentally tripped over a cord, losing all progress towards building the stage. The entire level had to be rebuilt from the ground up, and this may be part of why there's little thematic unification between Top Man and his stage (which, as a giant greenhouse, seems more fitting for a plant-themed Robot Master) outside of one mook and a series of spinning platforms near the end of the stage.
Trivia / Mega Man 3