I'd rather have Trade Companies than Colonial Nations, but I think for that to really make a difference, they'd have give trade in general a significant update. It's far too basic for Trade Companies to really mean anything more than trade power and annoying pop-ups at the moment.
Two words: free merchants.
On topic: I think the game could use a much more generic colonisation and subject model, and unifying trade companies and colonial nations would be a good start. There is no reason why an advanced Asian nation should not be able to create colonies or trade companies in their European colonies, for example. Lack of trade companies gimps Asian nations pretty big time, Europeans have the potential to get several additional merchants over Asian or African without much trouble. Similar arguments can be made for American countries and CNs, which also provide merchants. In my opinion, the player should have the choice of whether to directly control a province, add it to a trade company, or delegate it to a CN. Considering that CNs colonize on their own and are essentially vassals without a diplo slot, there would be a significant incentive to create them. I would also like to be able to annex them again.
Independence revolts should be handled by a generic system that would also allow for independence wars in Eurasia and Africa (maybe along the lines of the Dutch revolt that is already in the game). This would have the added advantage of making the late game more challenging.