Hey there Olleus. This looks like a highly ambitious project, and I wish you the best of luck. Aside from Impalers GP mod, you might also look at TheLopez's GreatPerson Trickle Mod.
If you have not already done it, I also think you should make cottages strip food from the tile on which it is built (I know this is the direction I plan to take). This might make cottages less of a 'no-brainer'. On a side note, I actually believe that 'Bigger is Better' has been largely eliminated, but that Cottage Spam has allowed it to sneak back in, so curbing cottages in this way might help to reduce this form of pseudo-ICS.
Another approach would be to tie resources and Empire size together via efficiency. This is something I have put forward before, where the ratio of resources to number of cities impacts on things like population growth rate, building rates and city maintainance costs. Once you are having to rely on more than half a dozen resources, this effect is going to have a huge impact on the growth of your empire, and might force you to rely more on those smaller nations who have a resource surplus. Hope that makes sense.
Here is something to consider in regards to Morale and War Weariness.
-If you lose an unpromoted or conscripted unit, the war weariness impact should be greater than if you lose an elite level unit. However, victory by an unpromoted unit should have a greater positive impact on morale than if an elite unit wins a combat.
-As Always, fighting a defensive war on your own soil should boost morale and reduce the impacts of War Weariness.
Anyway, just a few brainstorming ideas. I wish you all the best in this endeavour.
Aussie_Lurker.