One thing I do not like about mission trees is the strong link between flavor and power they often have.
The quality of the content in the latest versions has been quite a bit higher than in the previous versions and I understand that it is almost impossible to provide such content to all nations at once. The unfortunate thing here is that not only do countries have widely different flavor standards but also widely different balance standards.
And I think this could be avoidable. A lot of work in mission trees is design, research, localization, etc. I think it could be possible to keep the power of mission trees and other game features on par with each other without doing all the work at once. For example instead of revisiting old mission trees, one could at least adjust rewards to a certain degree.
A good example here are the missions "Monopolize East Africa"(Mutapa) and "The Future of Trade"(Venice). The requirements of both these missions are not that different from a difficulty perspective. But for one you get a strong trade modifier until the end of the game and for the other you get a negligible one for 15 years. These kind of power discrepancies can be found in a lot of mission trees.
Obviously not every country needs to have a mission tree of equal strength. But as soon as formable nations come into play this also starts to affect player choices to a significant degree. And if player choices are too unbalanced and straightforward a large part of the strategical element of the game gets lost.
It is also clear that power and flavor cannot be separated completely, as there needs to be some incentive to complete the missions.
But the incentive probably does not need to be as large as the recent mission trees make it out to be.
Consider my current Mutapa into Mughals run:
I do not see why a single mission (which is easy to complete) needs to give me more development than the entire world has in a normal run. Don't understand me wrong. I do like the creativity of the new mission rewards and I also think that the new modifiers added are great and allow for a lot of experimentation. But this is an example of a reward which warps core concepts of the game (development) to such a significant degree that there is just no other country which can even come close to Mutapa when it comes to gaining a lot of development.
It also, along with other things like the huge number of autonomy in territories modifiers, contributes to problems with older game mechanics. For example in this game I have 100 maximal sailors. Why? Due to coding limitations the max sailor variable is capped at some point over 1.3 million (This is some form of integer overflow). If you have too many sailors you will only get 5 sailors per month. This would not be a problem, if it were impossible to actually get that many sailors in the unmodded game. But in this run for example this is easily possible. I have been over the cap for decades.
This power discrepancy can also lead to deficits in believable storytelling, which seems to be one of the goals of at least recent EU4 design. For example why can pirates plundering weapons from the Venetian arsenal utilize these weapons better than the Venetians themselves?
Another balance concern is obviously the stacking of modifiers and I do think Endgame tags are probably not the best answer to this. They are very inconsistent, as a lot of very strong combinations are still allowed, while some weaker ones are simply impossible. While one can definitely see that this is taken into account when looking at the new Polish tree, this is also another limiting factor on mission tree design for formable non-endgame tags.
I think it would be great, if there was more work dedicated on game balance. Also taking into account a lot of the lesser known quirks of the EU4 systems. The real power of ship durability serves as a good example here. Probably there are certain established ratios of modifiers which are used in designing modifier rewards. But in some cases like naval quality bonuses these ratios are just way off. There is a lot of room to make the game more interesting, if these ratios were rebalanced, as there are quite a few choices in EU4 which are actually no choices at all, if one just knows the game mechanics.