IMHO the source of most problems when it comes to Europe vs. RotW "balance" is how trivial it is to send doomstacks on the other side of the world. I don't know why PI never worked on that, doesn't seem THAT complicated and would even make playing as a European colonizer much more interesting because of the additionnal challenge:
1) Sea attrition should be a real issue,
2) transporting troops by sea should cost loads of money (they can't just feed of the land, you need to pay for the necessary supplies for the trip),
3) any province qualifying as "distant oversea" (but with a better logic for that, Caribbean shouldn't be distant oversea from South America) should have a ridiculously low supply limit, whether it's yours or not,
4) increased oversea maintenance,
5) almost inexistent or ludicrously expensive oversea reinforcement,
6) huge terrain bonuses for natives, particularly jungle and artic.
In the New World, that would fit very well with the new possibility of asking a colonial nation to start a colonial war on its own, as you indeed would have to rely more on their troops, sending reinforcements from the motherland only in the most dire of situations given the associated costs. Eventually you could have an option to manually take control of their armies, maybe by attaching one of your generals or regiments.
As a native that would obviously make your life easier (but maybe not much more interesting). Maybe so much easier that diseases would have to be buffed
