"The Wind Rises" portrays these moral qualms, when Jiro's dreams suddenly turn dark and ominous, when the pretty swooping biplanes suddenly morph into threatening heaving monsters bursting down through the turbulent clouds. Jiro's problems are technological in nature, and "The Wind Rises", similar to "The Aviator", patiently takes us through his various breakthroughs in construction and design (he gets an inspiration for curved wings from looking at a mackerel bone). The Zero fighter plane, which put Japan on the map in World War II, was a long-range aircraft with a high degree of maneuverability.
By the end of the war, technology had developed so quickly that the Zero was left in the dust by other fighter planes, and Japan resorted to using the Zero mainly in kamikaze operations. The film has been criticized for glorifying the deadly Zero, for glorifying Horikoshi and whitewashing some of the more problematic elements of his career. You could certainly make that case, and the soft-pedaling of what the Zero actually did in the war, and how it was used, is the only weakness in the film.