- Badass Decay: Envy. In the anime, he was a big enough threat that he killed Edward. Here, he's not only a dragon, but one in a world without Alchemy, and yet, he, very easily, gets captured by the Nazis and spends the rest of the movie as a Living MacGuffin.
- Complete Monster: Thule Society Chairman Dietlinde Eckhart is the Big Bad and an occult supporter of the Nazi party trying to reach the titular Shamballa to gain the power to conquer the world. Capturing Envy to open the gate to the other world, Eckhart keeps the homunculus docile by allowing him to bite into Hoenheim, leaving the man in agony. When Hoenheim sacrifices himself to open the gate, Eckhart, no longer needing Ed's alchemy, shoots him and leads an assault into his world. Enthralled with her newfound ability to use alchemy but fearing others with the same power, Eckhart tries to destroy the very world she once sought to conquer, a xenophobic hypocrite who would not tolerate anyone but herself having authority.
- Contested Sequel: Some fans view The Conqueror of Shamballa as a touching send off to the characters that ties together most of the loose ends left over from the series, and enjoy it for its share of cool moments. Others see it as a kick in the junk that resolves nothing and simply screws everyone over worse than they were screwed in the series, and also deride the film for its plot feeling rushed and the general feeling of inconclusiveness (particularly regarding series regulars Roy Mustang and Winry). The real real-world connection is also a big part of the contention: Some fans like that it puts the stories' messages, which are based on real historical and contemporary events, back into that context in an unmistakable way. Others think it cheapens the complexity and subtlety of the TV series.
- Fan-Preferred Couple: Edward/Alfons is rather popular, due to Alfons being an Ensemble Dark Horse and having a rather romantic interest in Edward (there are scenes that suggest he's upset that Edward is so eager in leaving Earth - in addition leaving him). In fact, shipping them together is way more common than shipping either of them with Noah, who was meant to be the center in a love triangle involving the three.
- Harsher in Hindsight: Ed's entire journey, revolving around returning to his world in the face of everyone telling him Amestris and alchemy are not real, has a different tune to it after the release of Fullmetal Alchemist: Brotherhood. With Brotherhood's release came a small new fringe of the fandom viewing the 03 anime as "not real". Though with this comes...
- Heartwarming in Hindsight: Alfons' words to Ed about proving Earth and its inhabitants are "real" and not "dreams" can almost read as an argument for the two Fullmetal series to exist side by side.
- Memetic Mutation: "They made Maes Hughes a Nazi!" or similar.
- Narm: The English dub brings back the entire cast back, which for the most part is great. The one caveat is Aaron Dismuke was very clearly going through puberty during the recording, so a lot of Al's lines come out awkward.
- The Scrappy: Noah, Rose's real world double, comes under a lot of fire. She betrays Ed only because she thinks she won't be discriminated in Amestris and then she turns on them soon afterwards when Eckhart shoots Ed. It turns out it's a good thing the writers didn't create the Ed-Noah-Alfons love triangle originally planned for the film: a portion of the fanbase didn't like her for taking over Winry's spot, and they would much rather ship Edward with Alfons instead, or with Winry.
YMMV / Fullmetal Alchemist: The Conqueror of Shamballa