I think Victoria 2 (And to some extend Crusader Kings) has some good lessons for the military system mechainics, specifically the idea of mobilising your citizenry and the idea of differentiating your soldiers based on citizenship as well. While the time periods are of course vastly different, some of what works in V2 would IMO also work as mechanics in R2.
Specifically, I think a system that enables the mobilisation of an army for a campaign, to then demobilise it when either a peace is reached or a specific time is up (Probably a soft cap on time, rather than a date-of-disband), would simulate the examples of citizen armies that I know of - mostly Greek citystates, early Roman campaigns, Carthage some times. Using an army like that obviously has drawbacks, such as a pressure to reach a settlement before the army goes home (Or the penalties for keeping it in the field grows too big). On the other hand, mobilising them and disbanding them are cheap choices, as they provide their own equipment and return to their farms. A mobilisation pool ought mostly come from right-cultured citizens. Unlike V2, you'd be able to recruit units from this pool, such as heavy infantry, cavalry etc., and mobilising is not an on/off switch. I don't envision these units reinforcing; they're not meant for long campaigns where that's needed anyway. The percentage and quality (Perhaps also available unit types) would depend on government type, national ideas and other proxies of martial culture. If there's a soft-cap on campaign time, this could even simulate the destabilising effects that the Roman system had over time, leading to social conflicts, reforms and civil wars.
If you want to occupy a hostile territory, an army that returns after a short campaign is obviously impractical. In that instance, you have to rely on more permanent soldiers. Standing armies and mercenaries are somewhat different, but they share the characteristics of being expensive to hire, maintain and disband. Standing armies come from POP types, but cultures, cores/civilisation level and NI's influence what kinds they are: Numidian tribal soldiers as well as Gallic cavalry and auxilliary troops may be the best you can get as a foreign empire, while you need your core armies from your own "freemen". Balancing the need to use your various pools optimally, you may opt for a system like the Romans, or shift your culture to accept Persian and Egyptian like Alexander did. These troops tend to become loyal to commanders over time. Mercenaries are already loyal to their commanders, of course, but will be demanding of your treasury and not your manpower pools. They will also more readily switch allegiances if you run out of money or military luck.
A tribe may be highly martial, and thus able to raise a lot of experienced armies the second they go to war, but don't have the economy to raise a standing army. Meanwhile, a highly centralised kingdom like Ptolomaic Egypt may not have the right culture to mobilise their Egyptian subjects, so they rely on a combination of Greek and wrong-cultured soldiers as auxilliary. Rome could do with the citizen armies for a century or two, until they have to permanently occupy most of Iberia, Tunis, Greece and parts of Anatolia. Suddenly the drain of keeping citizen armies mobilised and far away, coupled with a few high-profile defeats, saps their entire mobilisation pool. At that point they either have to face defeat or recruit a permanent army that requires land for pensions. Carthage could rely on own citizens for some units, but otherwise recruit from their non-Phoenician subjects in Iberia and Northern Africa. When their armies venture into Gallic territory, they can reinforce with Gallic mercenaries before crossing the Alps.
Are there historical examples that don't fit into such a system? Underdeveloped economies that field standing armies, for example?