I'd have to agree with you that is essentially the only real problem. I don't see any way around it but it really only affects the game in a few ways.

Bribing is tougher since all the units in a province aren't in one stack. It makes it more realistic IMO because I don't think bribing a whole country is really believable.


Also, it makes assassinating, spying, and inquisitions easier to "pick a target" instead of only the strongest guy in the stack. I kind of like this because oftentimes I don't want to go for the big honcho. Sometimes I want to pick off a prince who is lower rank than the big boy and now with huge units he gets his own stack.



the stacking limit is weird in the sense that when you play with huge units, stack size is doubled, but playing with Normal units just upped to be huge the stack size is the same.

I tried playing with Huge units option but just cutting the price to one half, but they still always build in two turns. i don't know if you can put build time as .5 so when you play as huge units it will double it to a build time of 1. You could give it a try? I'm on break and I left my game at school so if you could give it a go and tell me what happens that'd be cool.