TBH I've found that this phenomenon of the challenge and interest decreasing rapidly as you expand your empire to be a problem stretching right back to Shogun, and in fact pretty much every strategy game I've played since the original Civ. I guess it's a Catch 22; the game is most fun when your back is against the wall, whereas when you are stronger than your opponent it always feels like you won through simple brute force. But playing the game successfully inevitably leads to a situation where you are stronger than your opponent. Unfortunately I suspect this is a problem fundamental to the very nature of strategy games. There are a few things you could try though to spice up the late game a bit.
When waging an aggressive war against a weaker neighbour, I quite often try, rather than sending my entire overwhelming force against them, sending only one powerful stack to attempt to take their cities one by one. This can get quite tricky, facing off against similar sized or larger forces and assaulting well defended settlements but needing to not only win but keep your force mostly intact in order to continue the campaign. It also has a bit more of a narrative campaign feel to it rather than taking every city on the first turn with a separate stack, which feels like a massacre rather than a war.
Here's another idea I'm considering trying but haven't gotten around to yet; if your empire expands more or less radially, one of the reasons why a large empire is so vastly strong compared to a small one is that there is a big economy of scale in it's defense: To defend it efficiently, you only need to garrison the settlements on the circumference, but all the cities in the empire are producing money, so a large empire will be able to defend at a much lower cost per city. In short, the financial output of your empire increases at least as the square of the radius, while the cost to defend it increases only linearly.
My idea would be to expand your empire in such as way that every province would need to be defended. The way to do this would be by only taking provinces which do not already border one of your existing provinces; for instance, if you hold Nottingham, then London, Caernarvon and York would all be off limits, but Edinburgh would be fair game. Thus you would end up with a patchwork of isolated provinces, each responsible for its own defense. You could expand to acquire quite a large empire this way, but it would be a large empire without all the economies of scale that normally make large empires so overwhelmingly strong; all of the cities would need a proper garrison, there would be no "safe" hinterland that could be left with minimal defence; it would be impossible to maintain a strategic reserve to ferry to hotspots due to their isolation; expanding cheaply would be hard since it would be impossible to do so without leaving undefended borders, and it would be difficult to specialise settlements as "cash cow", "cavalry training center", "siege weapon factory" etc since every settlement would need to be an all-rounder to some extent.
Plus, it would bring all whole host of extra challenges; your income would be almost entirely dependent on trade with foreign factions, meaning good diplomatic relations would become an actual necessity rather than a luxury. Also, sharing so many borders with so many factions would be pretty much an enticement for everyone to attack you sooner rather than later.
I'm still trying to think of a snazzy name for this campaign, maybe "the Patchwork Campaign" or perhaps "the Four-Colour Campaign" in honour of the related mathematical problem.
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