I have a small problem with your post, in that you start it with "you like mission trees" but I feel like you end up defending the concept, and individual small ways it was implemented, rather than the system in the game as we have it overall.
You are absolutely right that some form of missions wouldn't be bad. I like your example with HRE minors. I quite enjoyed doing the mission tree for Lubeck, as it didn't try to too much wild stuff, it didn't go too far into the game(it mostly covered your first 50-100 years) and didn't gave you overly op bonuses (still too strong for my liking).
This is a minority of mission trees in this game at this point.
The challenge of playing most nations, especially ones reworked in more recent patches, has been almost completely negated by what you are now provided with MTs.
Poland, for instance, was already a country with one of the highest military potentials even before their first update back in 1.27. The 1.33 mission tree made them so hilariously broken, Poland now feels like an anime protagonist surrounded by measly tertiary characters.
Mutapa used to be a tougher-ish start, given its placement in Africa, but now hey you get a mission that makes you get dev for building buildings.. which makes you earn more money for more buildings for more dev. Sure, it's "cool" I guess? but it's also incredibly brainless.
It adds to the game at the expense of turning other parts of the game irrelevant.
Oh cool, I now have magical wizard funi horsies that can cast avada kedavra on their enemies, but now the entirety of warfare & combat boils down to just moving an army on top of your opponent's army without thinking.
I have a cool mechanic that makes me stronger by building buildings.. but now I don't need to worry about not being able to afford things, because that mechanic gives you one of the most insane snowballs possible in this game.
This is more important than I feel you might realize. The AI doesn't complete its mission trees because it straight up doesn't know how to.
Mission trees are nearly exclusively a player-only mechanic. Almost anything that you get through a mission tree can be considered an unfair advantage over other participants in the game, that being AI for most players.
It is wild to me that we're seemingly fine with the player countries being made massively stronger compared to AI in EU4, when it's supposed to be a strategy game.
It's like we played chess, except I get a 3rd row of pieces consisting solely of queens. Enjoy. (yes, I get that EU4 shouldn't be fully symmetrical, no it doesn't mean that EU4 should turn into an arcade game).
Moreover, sure, I can agree mission trees can be just skipped. Let's ignore just how not great it feels to do that.
Doing so, would mean that the game for me has remained functionally nearly unchanged in 2 years, and in some aspects got even worse.
As you also indirectly pointed out, almost every single "cool" thing we've been getting is locked behind mission trees.
If you really push it, I can agree that complaining about MTs existence is off, but in this case I think it's fair to complain that better things don't exist in their place.
You are right that mission trees added come cool-ish mechanics, which in turn slightly alter the tired gameplay loop
but... why do they have to be locked behind following a railroaded storyline written by someone else, and why can only I get them, and not all the other participants in the game - like AI?