List of things not to model
It's not possible to model everything. Here's a list of possible things that could be modelled, but which I consider less important:
arms trade
religion
merchant fleet (size thereof, commandeering ships from, etc)
civil war/unrest/revolt/revolution/etc
coup d'etats
species/races (useful for a Lord of the Rings style scenario)
zombies (not just like normal side, as all inhabitants of conquered squares are turned into zombies)
multi-level (as in Civilisation II: Test of Time) (perhaps Surface, Seabed/underground, Deep underground, Deeper underground)
multi-planet games (with portals, etc)
government forms and government changing
the impact of changing tactics on unit strength
mercenaries/foreign legions