Pyramids changes everything as usual

However, while representation changes the number of beakers per specialist (2x scientist = 12 bpt under rep), it does nothing to the multipliers. It only changes cottage / scientist balance (towards more scientists and less cottages).
So you can get 60 raw beakers in many ways. Maybe you get 12C from trade routes, 48C from tiles, and run the slider at 100% (OK, you need more commerce). Or maybe you have GL and run rep + caste with 5 extra scientists (total now 7 x 6 or 42 beakers) and get some more from trade and for working riverside food. Or maybe you're running bureuacracy and with the 50% commerce boost your capitol easily gets 60 raw beakers?
Still, I'm not saying that you need 60 raw beakers now. Just that the city should "fairly soon" reach that. A city that won't get 60 raw beakers ever doesn't really look like an academy site, but one that is already working half a dozen cots and will get to a dozen given calendar happiness (or other happiness) just needs some time as the cots mature and free speech will eventually make it a commerce monster.
Oxford changes two things again: multiplier, and #scientists the city can run (without caste). Unless we're talking about food-heavy city, it'll be hard to get past the two scientists anyway (pre-biology - when you do hit bio you can again run more specialists). So Oxford should eventually be built by a city that benefits at least from one of those, preferably both (eg. those dozen cottages and 2-3 food resources). Incidentally, this city is likely to be good science city already before Oxford is built, so academy is likely to be in order in any case
My basic reasoning behind setting some rule of thumb for academy is that I probably (hopefully) will be getting several Great Scientists in the game. And I can do many things with them: academies, settling, bulbing, golden ages. Spending a scientist for a GA seems like major waste, but the other three have their uses, and a choice between the three must be made.
Lightbulb: instant benefit. That is, if I can bulb something that is useful either directly as a tech for me, or for trading, or even for both. If my research is very strong, bulbing might not be that useful and academy is more likely even in case where bulbing is a strong option. However, getting those beakers NOW, not during the next 100 turns, is often a big benefit.
Academy: if I have a strong science city (or one with lots of potential in the future) and don't have an academy yet, this is a very good choice.
Settling: If I have a city with an academy, I'll consider my other cities. I might have more than one strong science city, so maybe more than one academy is in order. However, once the major science city has been marked and academified, the beaker multipliers will make settling a strong option. While an academy provides +25% beakers, a settled GS provides 6 to be multiplier. Assuming library, university, two monasteries and oxford, we're talking about roughly 200% (and while the monasteries will be obsoleted, observatory will cover the gap keeping it at around 200%), so settling would be around 18bpt - 27 with representation. In the future. Maybe 9 (library + academy) to 17 (rep + library + academy + 2x monastery) now. For 25% multiplier to be better, four times that would be needed in raw beakers, which comes to 35-75 now, 75-105 in the future. Better be a strong second science city for settling in primary science city to lose against second academy.
The hardest dilemma is with the first one, assuming bulbing isn't a direct winner. Do I have a strong enough science city already, or is my Oxford city still in the jungles waiting to be settled (or inconveniently for now in the hands of an opponent, maybe called "Cuzco" or something like that)? Is one of my current cities going to be a strong enough science city that academy would be best?
I really hate storing the great people for the future. Each turn they spend sleeping in my capitol is a turn they coulde've provided hammers, beakers, gold.. settled, bulbed, using special ability. But at times I really can't find an academy site in my early empire, and still have ways to go until bulbing would be good enough, so maybe settling now would be best overall?