A revamp of the pop system, immigration, and the economic model:
1) Manual pop splitting is evil.
2) 100,000 pop producing 3x more (or whatever it is) than 100 pop is non-intuitive.
3) Having pop conversion cost the same for a 100k pop as for a 1k pop is non-intuitive.
4) American immigration should be more diverse, with people going to established industry, open RGO's, and gold rush states, rather than everyone going to one place. The game doesn't seem to model the westward migration very well.
What this boils down to is that the pop system appears to have been put into place in order to allow detailed and intricate handling of population migration, but the industrial model doesn't work very well with it, and the way pops move is unsatisfactory.
I am a constructive player rather than a warmonger. I am from the USA, but the reason I play the USA in this game is not nationalism, it is that I like to build stuff rather than conquer stuff, and the USA is about that during this time period, not that the native Americans and Mexicans and Spaniards would necessarily agree. It is possible that the pop model is fine if you play a European country, but it it is inadequate from the perspective of a habitual player of the USA.
I would suggest that the whole pop system be scrapped and re-invented, in order to achieve a more sensible model of industrialization, population growth, and population migration.
Without reading the whole thread, I'm assuming that a lot of people wish for even more intricacy (more goods, more detailed events, more unit types, or techs, etc.), and that would be my second list item.
My third item would be a true hands-off game, where I can examine everything as it is happening, and not have to play a throw-away nation in order to do it. I would like this in all Paradox games.