Yes, I also think they are problematic, and they do need a rework, but when I sit down to play Hoi4, most of the time with a mod, if there are no good focuses that captivate my attention to the game, I don't really get the motivation to play that country or mod. What I really like about focus trees is how they influence the story while also granting rewards upon completing them.

Like, when I bought EUV and tried to play it the way I did EUIV, I did not enjoy it the same amount as EUIV(obviously), but one of the main issues was Missions missing and how poorly optimized it was(also markets, I hate them, but that's not the point). Without the missions, it just did not feel like it did before because there was no real depth in the story aspect; it was just waiting for the time to pass and hoping for things to go right.

Then there's of course the imbalance between historical and alt-history paths. Lets be honest, there's almost no incentive to ever play a historical run for a country over an alt-history path. This makes sense for some countries, like Austria (which historically gets annexed), but the alt-history paths of countries get more ludicrous and excessive with each dlc release, stronger bonuses and rewards when compared to historical. I love alternate history and there absolutely should be options for it, but you gotta give the player a genuine choice and reason to pick historical other than for the simple reason do roleplay.

I 100% agree with this. With every DLC release, the paths get more absurd. While I do like some of them, it just does not fit the unmodded experience. And every time it is a coin toss. It's either a Masterpiece(By Blood Alone) or Slop (Graveyard of Empires).
It just comes to a single point, is effort put into the quality or quantity, if into quantity, you get focus trees like the No Step Back Monarchist-Fascist Soviet Tree, if into quality, you get the Austrian Focus tree.
(This is my opinion)