If you win the campaign as a pro-Imperial faction, you have just resurrected the concept for the Emperor's divine right to rule over the country. Which set the stage for the rise of the nationalistic and aggressive Imperial Japan, allowing the fascists to take over the country in modern times half a century later. Meaning your actions will indirectly lead to horrors such as the Japanese subjugation of Korea and the Second Sino Japanese War, which ultimately ends with two atomic bombs dropped on the country.
If you win the campaign as a pro-Shogunate faction, then you have just prevented Japan's transformation out of the traditional feudal system and the dissolution of the Samurai caste (who are no better than feudal knights), an outdated system that is both incredibly violent and oppressive to the majority of the population. By you winning, you have effective turning the clock back for another two hundred years and stopped the country's modernization right in it's tracks.
Not necessarily, considering how the pro-Shogunate side tended to be more accommodating to Westerners. If anything, a victory for that faction would most likely have Japan end up either as a buffer/puppet state between the Western powers or modernize anyway while retaining the pretenses of the old order.
Which leaves us with the Independent/Republic ending. It gives you a small Hope Spot that perhaps you can have a chance to prevent Japan from making all the mistakes that they made in our timeline by transforming the country into a democracy without the need of a devastating world war. However, in the victory cutscene, you were referred to by your general as 'our mighty leader', instead of, say, 'Mr. President' or 'Prime Minister'. Strongly implying that instead of creating a true constitutional democratic state, under your rule the country will become nothing more then another People's Republic of Tyranny.