Maybe what makes them good isn't scale independent.
Functional features of human organizations generally aren't, after all.
The idea that success == expansion is a capitalist (or even more narrowly, Wall Street) ideal and Universities should not be run like businesses.
Well, is it capitalist really, or is it something that capitalists are guilty of propagating as a means of control?
I mean, it could be said that 'success == expansion' is more of a natural law, which can be applied to any 'ism and used, either to contract agency, or .. grow it.
Perhaps there's a practical reason - maybe they can't find enough professors of the quality they want to teach any more students, but last I heard, professors weren't in short supply, especially not when you have $15 billion like MIT does.