The US Americans are known for their patriotism, yet their states bear a high a level of autonomy. Just because there are different states within a nation, it does not mean that the people are only loyal to their own state. Also, your comment on the Emperor of Japan only applies to the long age of Samurai rule before the Meiji Revolution and after World War II. The Emperor did have powers during Imperial years, he was simply not inclined to utilize them a lot, lest this might interfere with his sacred status. Maybe federalism would have changed history in that regard also and retained him as a mere nominal authority, but the patriotism that sprung up in the 1860s suggests otherwise. Another historical reality you should consider is that regionalism would always flourish alongside nationalism; it is simply a matter of the balance between them. Even after the Meiji Restoration the winning domains of the Boshin War, especially Choshu and Satsuma, continued to dominate government and military positions well into the 20th Century. They served just as much their own province as they did their country. I concede that solid decisions would probably be even harder to take on a national scale, but on the other hand it was to a large extent the overly powerful centralized military which gave decision-takers a hard time during the reign of the Empire of Japan.
There's a significant difference here which speaks to the advantages of the centralized state that the Meiji oligarchs supported.
Namely, to take the example of America, patriotism does not enter into the equation so much as a difficulty of the federal government in imposing its will on states, who have their own ideas about what policy to follow. In it's original form, the government could not do this at all, now, there are clear divisions of power, divisions which, for maximum warfighting efficiency, are actually dropped during wartime, and which in peacetime, arguably limit the efficiency of the government in imposing its will.
That was precisely what the Meiji oligarchs feared. If the nation could not fully deploy all its resources in the service of the state, as was basically the case under the decentralized feudal system, and which they saw as the case in a decentralized modern state, then the nation was that much weakened. Patriotism does not enter into it at all, what matters is the basic strength of the central government.
The Choshu-Satsuma dominance is also not particularly relevant. That a large part of the top leadership was drawn from one part of the country is not the point so much as that that top leadership ruled a united country. When you got right down to it, the Choshu-Satsuma dominance was not a case of one part of the country plundering the other part for their own benefit, but in fact, merely concentration of leadership among one group. It's not that different from a parliamentary system where at times, one party maintains dominance over the other. In short, the point isn't particularly relevant at all.
Basically, what I'm saying is that to the Meiji oligarchs, and in Japan at the time, what wasn't necessary, or not only necessary, wasn't national spirit alone, but also a strong central government which could totally mobilize the resources of the country. In short, there's no reason to support federalism instead of centralization, since there are few benefits, but large drawbacks towards the Meiji oligarchs desired goals.
Ironically the central state envisioned by the Japanese was at least partially inspired by the Chinese dynastic empires, however, it is true that Qing China's factionalism was a key factor in making it vulnerable to the Western and Westernized imperialists.
On the subject of heavy military funding I would like to say that the Japanese domains in total had larger military forces than the early Imperial Japanese military. The military powerhouses of Satsuma, Choshu, Tosa and Aizu made sure of that. I could safely speculate that at least initially, militarily a federal Japan would be more intimidating than a centralized Japan, with each province funding their own military.
But that's not at all conducive towards the Meiji oligarchy's goals. What mattered wasn't having 7 armies of 10,000 soldiers who were vaguely loyal to some concept of Japan, and also to a Daimyo, it was having a strong army of 50,000 which could defend Japan's independence. Factionalism
is important here, mostly towards the end of making sure it doesn't detract from the central government's ability to govern. The West knew this too, the first option makes Japan inherently weaker, because 7 armies under 7 commands is not as effective as 1 army under 1 command. So you 'cannot' safely speculate that a federal Japan would be anything other than militarily impotent.
I disagree with you on a second revolution. I merely said that Japan could create a federation. This does not mean they would retain a feudal system. After all, the Tokugawa State was not a conventional feudalism by any means. Lords were appointed and not necessary hereditary. They were in many ways more like governors than feudal nobles. Japan was well set to turn domains into federal states. A federation does not interfere with the popular movements of the day such as liberalism and ultranationalism while the Japanese were anything but religious even in those days.
Which is not so much the problem, so much as the fact that preserving regional differences is weakening a Japan at the point where it is absolutely necessary to ensure it is as strong as possible. At this point in time, the Meiji leadership's goals were to build a central Japan with a single-minded devotion towards Japan. Division does not serve this goal in the slightest.