MP is basically the reason why I still play EU3 instead of EU4; it's poorly executed and illogical. The illogical aspects of it is what pisses me of the most actually, e.g. spending MIL to get good leaders and good military infrastructure puts me behind in military tech, investing in good infrastructure gets me behind in administrative techs etc.
I would like to see them merge all MP into one, call it bureaucracy points or something. Then you can make the monthly gain be dependent on government type, tech group and ideas, with bonuses given by advisers and a combination of monarch stats. After that, create percentage based discounts on buildings, coring and such dependent on your monarchs stats and advisers.
Example: You are western tech group, which gives you 10 points a month. Your government type is administrative monarchy, which gives a bonus of say +5 points a month.
Furthermore, your monarch is 6 Mil, 7 Admin, 3 Dip; as one way of doing this, say all stats combined/2 is your bonus points for monarchs, so you get a further 8 points. You also have a lvl 1 adviser that gives you another 1 bonus points.
We can also say you have an administrative idea giving you +2 points bonus. (ideas could give you discounts or bonus points depending on idea group)
In total, you now have 26 points a month to spend. Buildings still cost points to use, and are separated by category, but they all use only one type of points. Now the monarch stats come in to play - each point would give you say, 5% discount, in a given category. So building an armory with your current stats would give you a 30% discount in points required, meaning 7 points instead of 10. Administrative stats would make building a temple 35% cheaper in points, etc etc.
Ideas could also give you discounts in certain categories, so investing in military ideas would decrease the costs of military techs and buildings, but your other techs and buildings are more costly than they would be if you invested in other ideas. Some ideas like administration could give you bonus points instead, which would make them useful across the board, but less useful for specific areas.
As you get more ideas and better government types, you get more points, so cost of buildings increase in scale - e.g. a regimental camp could cost about 100 points as base cost. This also makes it rewarding for certain playstyles. Say you invested in Mil tech and ideas and got an extra 10% discount on Mil buildings - with the current monarch you'd get 40% discount, making it cost only 60 points instead. At the same time, your investments in a strong army have made it more costly investing in Dip-type buildings and actions since you hardly get any discounts, making you weaker in that field.
Can throw in other modifiers via events, or make bad monarch stats add % to cost instead, or whatever tweaks necessary. Anything that rewards the player for their investments in an area, rather than making them technologically weak (or vice-versa, tech making you weak in buildings) for investing in it, needs to be implemented.