* AlternativeCharacterInterpretation -- Is Sternhart a thieving, arrogant JerkAss, or a respectable "fellow seeker" as he put it that is tragically KilledOffForReal?
* BetterThanCanon: Some fans consider this to be the ''real'' [[Film/IndianaJonesAndTheKingdomOfTheCrystalSkull fourth film]] of the series.
* HilariousInHindsight: For all the chiding ''Crystal Skull'' got for revealing [[spoiler: that the skull belong to interdimensional beings. The comic book of this game, made years before that movie, revealed the whole Atlantian society was inspired by ''aliens'']].
* SugarWiki/NoProblemWithLicensedGames: Some fans even state that the game is [[BetterThanCanon better written]] [[Film/IndianaJonesAndTheTempleOfDoom than two]] [[Film/IndianaJonesAndTheKingdomOfTheCrystalSkull of the films]]. It helps that [[AdventureGame the genre]] tends to parallel the pacing and writing structure of film more than other gaming genres (assuming you're not [[MoonLogicPuzzle getting stuck]]), allowing for a story that can feel like the movies without relying on GameplayAndStorySegregation.
* ScrappyMechanic: The balloon ride and the submarine-steering scenes. The fighting could also be considered this, since this is an AdventureGame, but most of the time it can be skipped by using the "sucker punch".
* SeinfeldIsUnfunny: The voice acting is full of DullSurprise and OohMeAccentsSlipping. It's important to note that the voice acting was a ''bonus'' for people who had the correct hardware at the time.
* ShaggyDogStory: [[spoiler: Dr. Ubermann ends up finding Atlantis and, in a fit of megalomania, tries to transform himself into a god. The attempt atomizes him, and causes Atlantis to destroy itself once again. Indiana Jones being there doesn't really change any part of the story. At worst, the Nazis might have made off with some Orichalcum beads before Atlantis went tits up.]]
* ThatOneLevel: Both the Balloon ride and the labyrinth navigation are disliked for being long and silent.