I actually like the new system, it is more logical. Though some tweaking may be necessary.
I see your concerns, but I think you exaggerate the problem (based on your specific case) and you do not even focus on real problem that is the often big de-sync between the institution spawn and penalty. A bit lesser problem is the balance in institutions spread.
Colonialism really needs tweaking, as it may spawn too late, in “unlucky” location and spreads badly. This may break the balance in MPs in 16th century.
Also some %% and MPs spending prioritization may be tweaked a bit, but this does not seem to be a major problem.
AIs pays more for techs across the whole game, like more 5000-10000 mana points than before. This AI mana isn't going to ideas, deving, coring etc. So AIs got massively weaker by this change. They neeed more time to get to the same point than before (time gets those lacking points).
I think this is just an unintended effect of the change. Hard to imagine devs trying to wreck AIs and at the same time saying they're working on improving them.
I see your concerns, but I think you exaggerate the problem (based on your specific case) and you do not even focus on real problem that is the often big de-sync between the institution spawn and penalty. A bit lesser problem is the balance in institutions spread.
Colonialism really needs tweaking, as it may spawn too late, in “unlucky” location and spreads badly. This may break the balance in MPs in 16th century.
Also some %% and MPs spending prioritization may be tweaked a bit, but this does not seem to be a major problem.