Only real complaint is the politics system. It's not defendable at all, it's pretty useless and doesn't really do much except inconvenience you once or twice later on in the game anyway.
Navies are fine, transport fleets can't move that far and the ships can't even ram and have almost no HP. Even if you're outnumbered with your fleet you can pull it off or autoresolve will be greatly in your favour anyway. All it needs is seasickness from Attila, honestly, to cripple unguarded transports even more.
One General, One Army system is how it's gonna go, no amount of complaining will revert it. It's perfectly fine in EE, do we need any more screenshots of ETW's Ottomans and their 5000 microarmies to prove a point? If you don't like it, you don't like it, but the system works fine.
If you turn your generals into errand boys to shuffle elites to the front, I don't know what to say, really, either, it's never been an issue for me that I've resorted to having to do that (when just using that general to raise an army is enough) and you have options from recruiting lower tier troops, building better infrastructure to support your war, or just mercenaries to fill in the gaps.
1TPY is fixed with EE, I never had issues with agents or generals anymore. They last a good 60+ turns before dying naturally, which is more than enough considering the average campaign lasts ~200-250 turns anyway.
UI is garbage, I'll give you that.
Filters you can mostly mod out or use an injector to help with that. Otherwise, personal preference. They're mostly there for local flavour. Mediterranean maps and Northern Europe maps and North Africa maps and Far East maps all have their own filter for a reason.
Battles last plenty long in EE since they boosted morale, slowed down killing rates by pretty much removing Bonus vs. Infantry on nearly all sword infantry (making swords vs. spear main lines fight it out much longer instead of swords massacring spears in melee). Most large battles can last a good 10-12 minutes now.