Very neat looking screenshot, especially the coast.
Another thing to think about is multiple maps, or layers. I loved how CtP had the space layer above the regular terrain, that alone was so cool. Using that kind of layer system would allow fantasy mods to have an underground and sky, like ToT and, would give sci-fi mods a double zoom kind of system/galactic or planet/system/galactic view.
And about the conquests problem, perhaps the 'occupy' could be a stage between enemy controlled and player controlled, which would give the enemy some time to recapture their city with all the culture and improvements, replacing the resistance phase. Individual mods could change how long this period is, or a player could be prompted to actually annex the city, which would add financial burden and would anger the mother country. You could purportedly keep it occupied forever, or barely any time at all, or give it up to the mother country for cities they occupy, or even set up a puppet government. That's a whole lot, but it would be very cool.