Funny thing - for me all of these you mentioned are things, that make Vic3 more fun, and more challenging. It's good, that there are limitations, and that player can't dominate the entire game through skill (or rateher AI's lack of skill) alone. It's nice and refreshing, compared to other PDX GSGs, like CK3, where going from Count/Landless to Emperor in one generation is no big deal.
Illiterate nations SHOULD be almost impossible to catch up in Research. Look at the most famous example of "catching up" in the timeframe - Meiji Restoration. It required total reform of contemporary feudal social order, immense education ivestment, obtaining lot of foreign technology (through sending own students to study abroad, or inviting foreign scholars), while also being strong enough to not let GPs abuse them. Not an easy task. And we're talking about relatively literate Japan, with strong demographic powerbase, and good defensive position.
Conquest, for me, still isn't limited enough. GB is going to side with another nation, just because they can. Because why would they want some other country to grow in power, to potentially threaten their domination in the future? GPs should generally want to keep power balance across the world, and that's what they historically did, as it assured their dominance. Keeping player's emerging power from growing is what XIX century powers would rationally do, and what you, as a player, would probably do, too. There's no reason, why should AI GPs take it easy on you.
Your last point was about military. Not letting you "skill your way from a losing position to a winning one" is one of the best decisions Devs made about warfare, as "skilling your way from losing position to winning one" in other PDX GSGs means abusing dumb AI's lack of knowledge of army composition meta, or tricking it into attacking you in mountains. Unfortunately, Devs still failed with their implementation of strategic-level war, and we're left with current micromanagemt hell in place of proper warfare.