My idea for solving late game dullness of being #1 is simple.

Every faction should have a set of homeland provinces, and empire provinces.

Your homeland provinces are loyal to you, and your nation and so are going to be your base of support, however if you expand from there you have an empire, and an empire is repressive. The Empire Provinces will be very prone to siding with a pretender to the throne, or conspiring to join a new faction, or joining with your enemies, banditry and piracy should also be high in empire provinces so not only will you need to deal with your empire provinces pretenders to the throne, but the bandits as well.

Civil Wars should also be with new factions like in RTW BI, not with simple rebels.

This will make it much funner to maintain an empire, since you will be busy, not with pesky peasant stacks and random rebellions, but with other factions, conspiracies to dethrone you, and conspiracy to hand over your land to someone else.

The penalty for empire rather then homeland provinces will go both ways though, so you will be able to easier get back your homeland provinces with less military involvement in reconquest, and it will also make wars much funner.