1. Better UI. At the very least it needs to be larger, and would be nice if anything that involves art, graphics, flags etc, would be little bit larger.
Following are not in any specific order, and #6 also includes what could be it's own number:
2. Customisable flags. Basically system from CK3, but for flags, with some expanded choices to allow us to have everything from heraldic insignia which were very common in EU time period, to simpler national flags later on. And for other cultures as well.
Please please also make it easy to mod! I know Victoria 3's system allows for lot of modding, but its not anywhere near as easy as going to paint and editing .png. Basically just allowing for option that allows every nation's flag to be customised like it would be your own would be perfect, i think in CK3 there is mod for that.
3. "HRE" like system available for all". So basically i don't think HRE system should be limited to HRE. In alternate timeline, there is no reason crown authority in France would not have declined and French duchies would have become more independent, and they would have ended up with system similar to HRE. French had hereditary monarchy and not elective, so perhaps Commonwealth would be better example, but still. Basically all large Empires could have become like HRE, and there should be mechanic for that.
Most importantly though, in my opinion HRE mechanic is just so fun that it would be awesome to get competing "HREs". These "HREs" should all be customisable to some extent. They should be able to pick and choose reforms, and either centralise into vassal swarm, centralise into regular united empire, or if Imperial authority declines, devolve. I am not sure exactly what customisation there should be, but
This "HRE" mechanic would be base which is used to represent at least federations, Japanese Shogunate, Chinese Empire and ofc Holy Roman Empire. They would start like they historically were, and have unique flavor, but would be more free to evolve into different directions. And importantly, new ones could dynamically form/be formed. And all of them could be different and changed and reformed.
4. Allow everyone to build their own great projects. Historical ones like Stonehenge ofc would be their own thing, but we should be able to build our own "grand castles" and such.
5. Less abstract modifiers. We don't need to go too radical here. But its weird how Viipuri for Finnish mission tree gets big defensive modifiers. Those would be more appropriately represented as a great project that gets built if you complete the mission. Same for Teutonic order's castles.
6. Less stuff which is just magically locked to some countries. Yes, countries should have their own flavor, and should be in good position to be able to (but not quaranteed) get what they historically got. But if another country manages to do the same, why should they be locked out? Buildings are good example, if i got the skill, i should be able to build it. And if i focus enough on doing something, i would become skilled at it, and get some modifiers which in EU4 might only be available from certain faction's mission trees. Finland is able to unlock powerful attrition bonus, i want to be able to unlock same bonus as other countries if i just am able to do so.
Land special units are another example. There is no reason i would not be able to form academy that trains my own special units. This would be costly to setup, but i should be able to do so.
And the regular land units, its good that we have some customisation over our armies. But there should be more substance to that customization. Rather than pre-determined units like "Napoleonic square" or "Mix order infantry" or "Reformed Steppe rifles", everyone should be able to build their armies to focus more on certain aspects, and this would be reflected in their units.
(7)Imo there should be some kind of dynamic military reform mechanic. When you reform your army, you could pick certain features to emphasise in your troops. For example emphasis on infantry defensive, cavalry shock and artillery firepower. Or all of them focus on one specific thing. In any case, your pips would be then determined 50% by what you focus on, and 50% based on your previous reforms. Longer you go before reforms, more skilled your units become at their current doctrine, but ofc eventually they will fall behind. So like historically, you would not want to reform during a war as nobody would know how to fight in new way, but you also don't want to keep using obsolete tactics forever.
You could also do things like focus on firearms early on, even though early on it would be better to go with something else. This would punish you short term, and reward you long term. Or do the opposite, be strong early, conquer a lot, then take the hit later, but still be able to eventually recover if you succeed.
So national ideas, events, mission trees etc should not have exclusive permanent modifiers that can't be acquired otherwise by anyone else, it should just give you a flavorful (and perhaps advantegous) path to unlock those modifiers in historical/historically possible manner.
EDIT: And national ideas and traditions and ambitions should be just what you start with, you should be able to change them later on. I love the national idea system but i would love it to be more flexible. For example i would love to change Finland's cavalry bonus to Sweden's infantry bonus (weaker early and mid game, stronger late game), altough things do need to be balanced somehow. I actually don't like space marines or super soldiers, i just like being able to tailor my country to be more like what i want, within limits of balance.
EDIT 2: I realise this post has become massive wall of text. If i have energy, i try to edit it into more compressed one later today.