do you run specialists in the universities?
what other buildings do you run specialists in?
how much pop per city than has a university? or should you be rolling in happiness by then and not need to limit growth?
I only work great scientist and great writer specialists. As for what pop, it's hard to give a concrete number, although generally you want to grow cities out as much as possible before slapping down a university specialist on them. Basically, if a city begins to work non food tiles, then its time to work specialists. And you are correct, once you get your idealogy policy its time to let cities grow how they please.
Testing this in a SP game with Maya, seems like you can get a deceptively large amount of science this way. It starts to seem slow around the Medieval period, but really comes into its own later. And I didn't even manage to land Jesuit Education because some AI grabbed it first (had to settle for Glory instead).
Jesuit Education is what allows you to quickly stack up mass science. Basically this is the benchmark for science per turn
No universities: 60 sci a turn
Universities up, no specialists worked: 100 sci a turn
Universities up, specialists worked, 160 sci a turn
Universities up, specialists worked, +2 sci per specialist, rationalism opener, 250 sci a turn
Universities up, specialists worked, +2 sci per specialist, rationalism opener, public schools, 500 sci a turn
Universities up, specialists worked, +2 sci per specialist, rationalism opener, public schools, factories up, 700 sci a turn
Universities up, specialists worked, +2 sci per specialist, rationalism opener, public schools, factories up, rationalism 17 percent from universities, 800 sci a turn
Universities up, specialists worked, +2 sci per specialist, rationalism opener, public schools, factories up, rationalism 17 percent from universities, Research labs, 1200 sci a turn
By getting Jesuit education, you create a snowball effect in which getting quick universities up leads to getting to public schools faster, which results in getting to research labs faster, and so on and so forth. With jesuit education there is no production delay where you have to spend 5-15 turns building science buildings. That REALLY gives you a huge tech advantage. Not to mention that trying to build research labs, and sometimes public schools, in an ics empire is a waste of time. You simply don't have enough production in most of your cities to get them faster than 10 turns in.