* AlternateCharacterInterpretation: [[spoiler:In the EX endings, did Eike not realize that preventing Homunculus from being created would cause him to not exist or did he knew and wanted to be free from eternal youth?]]
* IdiotPlot: The game's many puzzles and problems could probably be solved in minutes if the game didn't insist on making the player use obtuse solutions. It really doesn't help that whoever wrote the story seems to be completely unfamiliar with the very concept of time travel. Nonsensical paradoxes abound. For example, in order to stop himself from getting stabbed in the back, Eike decides to get a skillet. However, he decides that he just can't get one in the time period he's in, for whatever reason, and so he decides to go back into his past, appearing as a juggler he'd previously seen, and give a message to himself telling him to get a skillet. When he goes back to the time period he was previously in, he now has a skillet in his jacket. ''Except the player already went through that period and never got the message or the skillet.'' It just seems to appear from thin air. Logically, a future version of himself should've given him the skillet, similar to ''Film/BillAndTedsExcellentAdventure''. The list goes on. From going 400 years in the past to prevent a single tree from being planted, or changing an entire movie to avoid getting run over by a car.
* ViewerGenderConfusion: Okay, raise your hand if you thought Homunculus was female. Come on, don't be shy. Even his VOICE sounds feminine - and his voice actor is MALE.
** Not only that, it's Mario. Yes. [[SuperMario64 THAT Mario.]]