Ever wonder why mainland France is all of two provinces in Empire? note France proper and Alsace-Lorraine. It's because of the centralizing nature of Louis XIV's government.
In most of the games in the series, when you win the campaign, the ending cutscene will show how you have gloriously crushed your enemies. This is in sharp contrast to the entries that were set during or after the Enlightenment (Empirenote Especially if you are playing as a republic and Fall of the Samurai), in which it is a lot more melancholy, with you general/lord lamenting the human cost of his conquests and telling the citizens to never forget the military's brave sacrifices. This is most likely the result of Deliberate Values Dissonance between the different eras that the entries were set in. Considering that throughout most of history, war is both glorified by the state and that the general public of a nation didn't care much about war as long as it wasn't affecting them (It is highly unlikely that the ancient Romans or the feudal Shoguns cared much for the treatment and suffering of the conquered population). For games set during the Industrial Revolution however, there would have been an intellectual class who realized the terrible reality of war thanks to more widespread education, and it would have affected the ruling class' opinions accordingly one way or the other.
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 military 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of the traditional feudal system and the dissolution of the Samurai caste (who are no better than feudal knights), an outdated system that is both incredibly violent and oppressive to the majority of the population.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.