The only country where there is a major internal political issue is China. But the way they have the three factions system set up makes it odious for me to play. I tried it once, saw that I had no direct control over how I wanted to take the country, and quit that game. It's sort of the same thing for the Orthodoxy slider; I've still yet to find any game where it should be less than 100% religious (you need the manpower and the missionary buff to convert all the provinces you take; and the way the economy system works, you can lose the money without minding it).
If you are going to have any sort of internal politics, there should be better ways for the player themselves to manage it; it should not be left up to the whims of random events.
My own personal desire is to see more of a way to manage zealousness (single-state religion, single culture) vs. pluralism (multi-religious, multi-cultural tolerance). There are advantages to converting the heathen, but there's also advantages to Marcus Aurelius' advice to let the people keep their superstitions.
I also think that the whole AE/OE/Coalitions system needs to be thought about better. I had no problem with it conceptually, but the problem is that the game seems to keep way, way too much AE for too long. You can't burn it off in a century.
OE also seems odd, in that the game now works to make you engage in moderately-scaled wars for 4-7 provinces every few years. Get close to (but not more than) 100% OE. Lather, rinse, repeat.
Coalitions, as has been mentioned in other threads, really need to make sense. Random distant nations joining coalitions just makes for late-game sitzkrieg. I had a wonderful time playing Great Britain until about 1739, then saw the state of AE and the coalition built up, and.... then just deleted the whole saved game folder.
Speaking of which...
Feature requests:
1. "Make New Folder" and "Delete Folder" options under Save Game. Oh boy do I want to be able to save my games in different folders. I can do that manually now going into my machines' file system and creating folders, but why not just allow a player to instantly create a folder, or blow away a whole folder's worth of ancient saved games? Of course, there should be a confirmation button... but heck... This is not new computer science.
2. More modifiers for AE and OE. If you want to play with less AE and OE, to allow for more (or less) sweeping wars, let people monkey with these using sliders at game start. Either that, or allow some sort of national modifiers or event system to fire off, and create national or regional modifiers. ("Land grab in Asia!" 10% discount on OE for the next decade in Asian provinces; or "European regionalism stiffens..." 10% higher OE for the next decade in European provinces.)
3. More ways to *stop* "sabotage reputation." So far, the most I can do is create a the best anti-spy building in my capital. And... that's it? Come on! There has to be a way to make a secret police force, or a better embassy corps -- national decisions? Spend some Admin or Diplo points? I just loathe when some other nation can just lay down a sabotage reputation, and you have no recourse. I would love to also have it that, if the spy is discovered, it does far more than just remove the malus. I'd love to have some blowback in the spying nation's direction. Perhaps my allies love me even more, or the spying nation's neighbors trust him less?
In any regard, I should not want to just toss a game ever again in the mid 18th Century because of AE build-up and huge looming but ineffective coalitions make the game turn into an 80 year sitzkrieg. That's what 1.5 brought. I thought Paradox learned that lesson before.