Functionally - we need Japan to have less need of a large number of ready-to-go armies, so that they can't be used to overthrow the Empire - so we need to both learn from Japan and IMO the Roman Empire to get this to work.
I'd have to start with the stronger earlier Emperor theory.
The best idea I have on how is rather than have Samurai as another class, and thus a widespread source of military training and armies. Instead the early Emperors should use citizen soldiers for his army instead, Roman style.
It would be a drastically different approach to Japan - but you're looking at going all the way back to the Yamato period to do this properly. Have their expansion be built less on offering positions to the lords they are bringing on side, and actually dismantle the clans at that point. That could slow down the expansion, but there is an alternative that doesn't slow down expansion.
Have a large citizen army that the peripheral clans must contribute money and men to, but only in such a way that it 'tops up' the main army, rather than dominating it. This would enable the Yamato period Emperors to strip any rebellious clans of any power after they commit a crime. If done carefully, and land is never parcelled back to clan, they can slowly dismantle the peripheries, and use conquest of the rest of Japan to help pay for their troops/compensate them in some way. Perhaps having the idea that all land is owned by the Emperor, but essentially kept as leasehold by everyone else. - Some pay by military service, some pay cash, or some by unpaid labour as per the Inca/Egypt.
After that, as Japan is island based, other than some popular rebellion, it should be reasonably easy to keep it stable and governed. It just may end up having powerful bureaucratic families emerge. If the nearest thing to a professional army is kept in the capital and its environs, and controlled by the Emperor, it prevents far-flung warlords pulling a "Magister Militum" or "Shogun" on the Empire. This is how we learn from the Romans.
So other than rotating the army so that everyone participates at some point so that a BIG army can be called on in case of an invasion, the only other role for the army would be policing and overseas expansion - perhaps further north into other islands, OR into Korea and the Manchu regions (I'd suggest the lattermost first). It could be a way to offload overly popular generals/admirals/bureaucrats - let them start a new 'clan' in the conquered territories. Give them some of the forces as a personal dominion, and continue with the expansion by clan, with the same premise of stripping them of land with the main army if they break the law - that way these new 'Clans' deal with the difficulties of stabilising the territories, with the Emperor able to come in and strip them later.
It may leads to dozens of 'perfect clans' i.e. never breaking the law, with long-enshrined privileges, but it should prevent a Shogun from ever being dominant in Japan - a Shogun could arise overseas, but the idea of a Japanese Clan system policed by a Shogun overseas is preferable to one in Japan proper.
I'd have to start with the stronger earlier Emperor theory.
The best idea I have on how is rather than have Samurai as another class, and thus a widespread source of military training and armies. Instead the early Emperors should use citizen soldiers for his army instead, Roman style.
It would be a drastically different approach to Japan - but you're looking at going all the way back to the Yamato period to do this properly. Have their expansion be built less on offering positions to the lords they are bringing on side, and actually dismantle the clans at that point. That could slow down the expansion, but there is an alternative that doesn't slow down expansion.
Have a large citizen army that the peripheral clans must contribute money and men to, but only in such a way that it 'tops up' the main army, rather than dominating it. This would enable the Yamato period Emperors to strip any rebellious clans of any power after they commit a crime. If done carefully, and land is never parcelled back to clan, they can slowly dismantle the peripheries, and use conquest of the rest of Japan to help pay for their troops/compensate them in some way. Perhaps having the idea that all land is owned by the Emperor, but essentially kept as leasehold by everyone else. - Some pay by military service, some pay cash, or some by unpaid labour as per the Inca/Egypt.
After that, as Japan is island based, other than some popular rebellion, it should be reasonably easy to keep it stable and governed. It just may end up having powerful bureaucratic families emerge. If the nearest thing to a professional army is kept in the capital and its environs, and controlled by the Emperor, it prevents far-flung warlords pulling a "Magister Militum" or "Shogun" on the Empire. This is how we learn from the Romans.
So other than rotating the army so that everyone participates at some point so that a BIG army can be called on in case of an invasion, the only other role for the army would be policing and overseas expansion - perhaps further north into other islands, OR into Korea and the Manchu regions (I'd suggest the lattermost first). It could be a way to offload overly popular generals/admirals/bureaucrats - let them start a new 'clan' in the conquered territories. Give them some of the forces as a personal dominion, and continue with the expansion by clan, with the same premise of stripping them of land with the main army if they break the law - that way these new 'Clans' deal with the difficulties of stabilising the territories, with the Emperor able to come in and strip them later.
It may leads to dozens of 'perfect clans' i.e. never breaking the law, with long-enshrined privileges, but it should prevent a Shogun from ever being dominant in Japan - a Shogun could arise overseas, but the idea of a Japanese Clan system policed by a Shogun overseas is preferable to one in Japan proper.