You seem to have this a bit backwards friend. EU4 is much more reactive and lets you do what you please en route to accomplishing those goals (or ignoring them entirely). In HOI everything revolves around the focus trees, you are bound to them.
I'm all for more open-ended EU4 versions of goals, but HOI-style trees would never work with this many playable nations, the timeline, etc. Heck, I don't even think they're useful in HOI4!
I know, but in HoI4 you can actually choose which direction you want to go and the whole campaign is different depending on what you chose. In EU4 you basically only decide in which order you do these things. Also, as the focus system was there from the beginning, it has only enhanced and actually now allows more freedom than there were before.
In EU4, the mission system was dynamic before. It wasn't very good but you could choose from couple of different options and try to accomplish it to gain a little bonus. Usually you did not really pay much attention to the mission system in the big picture, but completed the missions as you were expanding in the way you wanted or which opportunities you had. Now it feels more like you are bound to follow the missions, which makes the game as a whole a lot less dynamic than it was, as it feels you have to conquer state X as nation Y and so on. And I know you really don't have to follow the missions if you don't want to, but they usually give quite good rewards now so usually you don't want to miss them.
The Worst part of the mission system I think is that often you want to save your mission rewards to a specific point in time which would make the reward most useful and then often claim many mission rewards at the same time to maximize your gain for purpose Y.
Both HoI4 and EU4 are sandbox games. The focus and mission systems adds restrictions to the sandbox aspects. I just find the restrictions in HoI4 a lot more meaningful a better fitting to the game than what we have in EU4 and what it is as a game.
I'm not totally against a mission system in Imperator, but I hope if one gets implemented, its a lot better than in EU4. I guess the right direction in Imperator would be to go with the dynamic system EU4 had before and then improve on that.