Newer Than They Think: The "Elephant Bathing Pool" scene as well as the scene of the rhino chasing a group of explorers up a pole were not in the attraction when it first opened. The two scenes (designed by famous Imagineer Marc Davis) were added onto the ride in 1962. Other sequences such as the gorillas trashing the camp or the tiger at the temple, were created for Walt Disney World's version in 1971 and brought back to Disneyland.
One particular example is a remix of Metallica's song "Nothing Else Matters" played during the prologue and Frank's backstory.
Complete Monster: Prince Joachim is a Prussian royal seeking petals of the Tree of Life to gain immortality. Threatening Dr. Lily Houghton for interfering in his plans, Joachim then kills almost everyone in the room for learning his name. Joachim later allies himself with cursed conquistador Lope de Aguirre to track the heroes, fully intending to betray him and his men so they remain cursed. Joachim recklessly fires at the heroes with no regard for the destruction he causes, and later threatens a native village to force the cooperation of Lily's brother MacGregor.
Critical Dissonance: Critics gave the film a rather lukewarm reception, with a 62% rating on Rotten Tomatoes. The audience, however, enjoyed the film much more, with a 92% rating on their side.
Fridge Brilliance: No wonder Frank was so stubborn against Nilo buying up his boat and the rest of the boats in town - Frank literally built the town, and cannot move away from the river. Without his boat, he can't make any sort of life for himself.
Not so much a genius bonus as Walt Disney trivia bonus but a lot of the lame jokes made by Frank during his cruise are straight from the ride.
Prince Joachim is a real-life historical figure and some of his actions are informed by the ongoing events of WW1.
Aguirre is also a real historical figure whose ill-fated expedition into the Amazon was most famously depicted in Aguirre, the Wrath of God.
MacGregor having two last names could be explained by English and Scottish naming conventions. More specifically, if a mother came from a prominent family, she could name her first son after her maiden name. MacGregor does mention in the film having cousins in Scotland so it would not be a stretch to think his mother's maiden name is MacGregor.
Jerkass Woobie: Aguirre is written as the archetypical conqueror who invaded an indigenous tribe’s land to get their power out of greed. Yet he had a sympathetic motive to save his ill daughter. He did nothing wrong until the tribal chief refused to give him the Tree of Life’s petals, and while the natives had good reasons, it's not surprising he snapped so hard given what he went through for his daughter's sake.
Nightmare Fuel: Aguirre and the other cursed conquistadors. Aguirre has snakes oozing from his body (including from his face when Macgregor cuts him), Sancho is covered with honey and bees and seems to be missing the back half of his body, like a lopsided hive, Gonzalo is made out of mud and Melchor is made out of treebranches, exposing his skeletal ribcage beneath his rusted out breastplate, with sharpened sticks pushing from his face like a beard. Aguirre's appearance when Joachim first makes the deal results in his face splitting apart and snakes rushing out before we cut back to our heroes.
Spiritual Successor: Comparisons to Pirates of the Caribbean were inevitable, but the film actually has much more in common with The Mummy (1999): An eccentric yet determined woman of science embarks on an expedition to uncover a legend she has believed her entire life. Joined by her bumbling brother, they set through unforgiving environment with the guidance of a lovable rogue, and are before long set upon by undead monsters from an age long passed.
It also has more than little similarity with the film The Mummy (1999) with a premise of a British female historian/archeologist who is not respected in her field due to her gender finds a clue to a lost macguffin and travels to find it with her brother who is a primary comedic relief, who team up with a American adventurer who has a history with the location of the MacGuffin in competition with a rival expedition for the prize, and on this quest they awaken a supernatural threat tied to their quest.
More specifically, if a mother came from a prominent family, she could name her first son after her maiden name. MacGregor does mention in the film having cousins in Scotland so it would not be a stretch to think his mother's maiden name is MacGregor.