Replacing the Old with the New
One of the main themes of the film is really "out with the old, in with the new", in that the old Shogun tradition of the Samurai is being completely sidelined and almost outlawed in favor of modernization in the form of Westernization. Emperor Meiji is young and inexperienced and not well-versed in political nuance. He is easily manipulated and Omura takes advantage of this so that he can trample over the legacy of the Samurai, whom he has resented since he was a young boy. The heritage of Japan is being thrown to the side in favor of what is considered to be progress, and no effort is being made to amalgamate old and new to form something different that moves the country forward but still honors its history and its heritage.
Honor
The issue of honor is so entrenched in the Japanese that they would rather commit suicide than be seen to fail, or be perceived as doing anything that might bring shame to their family. This is clear when Omura tells Katsumoto that he should kill himself after being arrested for carrying a sword in public; only a public and painful self-inflicted death is able to restore his lost honor. The public carrying of a sword would not seem to be a particularly heinous transgression, yet Omura hints that it is shameful enough to warrant such a painful death as slashing oneself in the abdomen.
Katsumoto believes that the honor that the Samurai have lived by for centuries is being both disrespected and usurped. Honor is one of the central tenets of the Samurai and from his perspective, the fact that his former pupil, Meiji, is now riding roughshod over the traditions of his people insult his honor and his integrity.
Westernization
The theme of Westernization also encompasses the theme of the willingness of businessmen such as Omura to make deals with outside interests if it furthers their own interests as well. One of the main elements of Japan's modernization is Westernization, primarily because Meiji believes that Japan is falling behind its western counterparts. He does not want this to happen and wants to make Japan a major player on the world stage. Omura encourages him to believe that this will never happen without significant Westernization.
Omura's enthusiasm for Westernization is driven by the fact that it plays into his own business interests. One of the main interests he has is the railroad; his transportation networks will be key in developing trade agreements with nations in the west, and so he believes that increased Westernization will result in increased business, and therefore increased financial fortune, for him.
