But actually here are some of my thoughts
1. Mechanics could be added to approval rating. Something like defection rate from the military, or uprisings like in CIV when revolutions happen if happiness is not held to a given rate. The approval system would obviously need to be re-balanced such that it isn't a massive impact on the game but it would add a bit of depth and flavor to city management.
2. Make policy decisions important. Right now just war policy and domestic policy have in game implications, but the whole "government type" as well as economic decisions are just kinda sitting there with no reason to tweak them. I understand that some folks like the self expression that being able to be a communist theocracy gives, and that adding implications to such political choices may be divisive based on how people view politics OOC, but again this could add depth and ways to develop more complex strategies or national identities. This could be intertwined with a new war system or tech tree developments, but in order to avoid total changes I would say time limits on changing policies would be good.
3. I'd like to second some of the blockade ideas. I think that they should block taxes, probably block credits (less important honestly), but I really like the idea of blockade runners, but instead of a pay to use system, it could be like bounties where it is player based. I.e. a nation hires another nation off of some board and based on the size/tech of the hired players navy some amount of res get in. The players could set their own price for running the blockade, but if the nation who is running the blockade blocks some or all of the shipment then they receive those resources instead. This can provide some importance to alliances as well as it risks alliance resources but can get needed resources in. I think this doesn't interfere with the way the blockade is normally used right now which is to keep res inside a nation so the goods get taken.
4. This also provides a golden opportunity to mess with navy mechanics, i.e. specialized boats. You can still have the same number of ships, but you must choose between subs, aircraft carriers, speedboats for blockade busting, destroyers. Heck, throw in a pirate ship. It also could balance the use of planes vs ships depending on the type (subs can't get hit, aircraft carriers dogfight, destroyers have AA, ect)
5. Ground control could also be fun to mess with. Targeting improvements seems like a no brainer, but I also like the idea of occupying a city. A play can send X amount of soldiers/tanks to essentially take control of a city and siphons those res/taxes to the occupying nation, but defending nation get a big bonus when trying to retake the city. Guerilla warfare and whatnot. If not city occupation, then some sort of ground control = land control where farms are seized.