Hilarious in Hindsight: For all the chiding Crystal Skull got for revealing 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.
Scrappy Mechanic: The balloon ride and the submarine-steering scenes. The fighting could also be considered this, since this is an Adventure Game, but most of the time it can be skipped by using the "sucker punch".
"Shaggy Dog" Story: 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.