I'd like to see it operate more like Vicky 3's systems, but still governed largely by your internal affairs (government and estates being the biggest gain - or drain, if there is internal conflict) and boosted, possibly significantly, by an energetic monarch. A movement away from a currency pool and towards a capacity. The most apt comparison to Vicky's functionality here would be Authority, as it's the most limited resource and the one most impacted by gains/losses - that's essentially how I want to see them function. The diplomatic aparatus of a popular King with a smoothly functioning interplay of Estate and Court behind him may be able to maintain six defensive pacts* and three vassals, say. But if that King dies and his unpopular son causes internal conflict, that same aparatus would creak under the strain, and you'd be forced to either sever some ties, loosen the restrictions on your vassals, or suffer some penalty, like a ticking malus to relations, or slower AE decay, whatever.
I also don't think they should be used for research, but rather influence how much benefit you get out of certain technologies, or how much "momentum" you have in reforms. I don't have concrete ideas for how this could play out, but if the system can simulate something like Peter and Catherine's attempts to reform Russia, which failed to carry on momentum past their deaths, that would be good. It should take a bit longer than the click of a button to make something like an administrative reform really stick, and become an integral part of the "identity" of your national governing bodies, and not just a quirk of that particular ruler's administration. This could also play into the back-and-forth between Estates and Government that my ideal EU5 would have.
*As an addendum, but one that doesn't have anything to do with mana so not one I want to discuss further in this thread, I think Alliances as they exist should be removed from the game and be replaced by defensive pacts. Offensive allies should be invited per-war, similar to Stellaris and Vicky, or be assembled in Leagues for things like Crusades, the Holy League, etc.