“People who design machines and airplanes {or buildings}, no matter how much they believe that what they do is good, the winds of time eventually turn them into tools of industrial civilization. They’re cursed dreams. Animation, too. Beautiful yet cursed dreams.”
― Hayao Miyazaki
It should be a central theme, but for 99% of the movie not a single character offers and opinion on the idea that they are making planes for a fascist regime during world war 2. There is so much lost potential in this film. Mitsubishi during the 30s and 40s was the equivalent of Lockheed Martin; if you are working there you are working to further the efforts of imperialism. Everyone working there knows from the beginning that they are producing weapons of war. Instead of having any focus on that aspect, the movie portrays the creation of these war machines as realising a dream with Caproni saying that Jiro built beautiful aircraft.
The Zero was the reason for Japan's air superiority when they took on China and South East Asia. It is also the reason they were able to pull off the Pearl Harbour bombings. It was also one of the main aircraft, if not the main aircraft used for the kamikaze missions. The real life Jiro had strong opinions on the use of his creations. He also had strong opinions on the war and experienced the consequences of the war first hand. Jiro would also work himself into the ground during the war and almost died from it while neglecting his wife and child. This is what I mean by how I was disappointed by how much was ignored. Miyazaki made choices to try turn the film into a fairy tale like story about the genius of Jiro while ignoring the circumstances that made Jiro who he was and what his creations turned into. Its especially weird because like the quote in this thread and in many interviews Miyazaki has always been adamant in his anti war stance.
Anyway, sorry for the rant
I think the scenes of violence interspersed into the fairytale story did a lot of the legwork. It's also important to remember that Miyazaki's distributor employs censors and a lot of his films are very carefully walking the line to make anti-war films that get past the censors. Sometimes it's well done, like Nausicaa, Mononoke, or Howl, and sometimes it's more ambiguous like in The Wind Rises.