Are the universities fine after the decades long algae bloom of administrators? Has admission become more merit based, tuition more affordable, inquiry freer, and the pace of scientific breakthroughs faster?

Wikimedia, as you may have noticed, is not a university.

It is not. But since you seem to tacitly agree that most of Wikipedia's enormous wealth is funneled into putting people into positions of power who are not predominantly motivated by furthering Wikimedia's core mission, I'm curious to hear your thoughts on when in human history this has worked out "fine" for an organization, i.e. without degrading or even perverting the pursuit of its original objectives? If it hasn't, what makes you so confident Wikipedia will be different?

Wikipedia indeed has some unique aspects that give it additional resilience from hostile takeovers, such as public auditability (via edit history etc.), forkability, and finally the fact that the bureaucrats have unusually little leverage over the lives of those who do the actual mission-aligned work.

But universities also enjoyed some unique protections (tenure etc.). The end result was that it just took a bit longer.