I like the idea of multiple Ai for every civ, with different traits.
On a Computer perspective, these Ai could work in unison, following a civ, or later National identity, or Agenda, until some Alien trait appears and Hijack the Military commander Ai and take full control over the other Ai, transforming a peaceful civ into a bloodthirsty one, or the contrary.
On a Player perspective there are already enough conflicts between choices of what kind of civ one wants to pursues, but it would be interesting to see your Army taken over by an Alien Ai and try a revolution on you, or else a bunch of cities declare independence because they developed their own language and identity and just trying to suppress them is bankrupting you so it'd be better lose them. That loyalty mechanic I completely despise when it's on me.
How would it translate in real world mechanic by other means? HK isn't really a mechanic, it's just an evolve feature. HK also has loyalty per city and it's not uncommon to see entire civs burst into chaos and disappear completely with no warnings whatsoever. Maybe it would be better to include more than one civ under your control, under one ruler, but still distinct.
You play as the 'Germans' that would evolve into many Nations and you could take control over all of them, or let them go... idk, interesting maybe a scenario or two could try work on this idea, but
I'd rather stick to the old model for at least the player perspective.