Biowell spam is a decent alternative to Academies if you have bad terrain, but otherwise I usually end up with slightly higher win times when going Bionics first.
I think the biggest problem is the increased food cost for population growth. That doesn't matter all that much at lower pop numbers, so Biowells can be a great kickstarter to get a city off the ground, but at size 10+ you start to notice the diminishing returns from excess food.
Essentially, the Academy allows you to convert 2
into 2
by working a Grassland tile. The biggest downside to the Institute is the high construction cost but you save on both
and
by not having to build and upkeep as many Workers.
Yes, that is essentially it: Academy vs. Institute is a money/energy issue.
I used to build Institutes in all cities with my Academy strategy, but I noticed that Scientists are actually more of an emergency option than a valid alternative. The food loss from employing them is significant and usually far worse in the long run than the ~2E saved from not building an Academy. So the only reason for me to use Scientists nowadays is terrible terrain.
You need less workers by using Institutes - but you can build those workers in your high-production cities anyway, while Insitutes require local hammers (and if you have the money to buy them you might as well spam Academies).
Overall, the Cognition tech and the Academy is really just of special interest to Supremacy players - just as the developers appear to have intended. Harmony players will be building the Xenonursery, so they have four Scientist slots total and not much need for Academies. Purity players will build Domes which are not far behind the Academy in terms of usefulness - these won't win as quickly against the AI but will give a more well-rounded game.
I don't think that Cognition was meant to be a Supremacy tech. Supremacy can get a bit more from it, sure, but I don't see how other Affinties would close the gap if they ignored the tech.
Those 4 scientist slots are enough to justifiy ignoring Academies (and not every city has Xenomass anyway). Even with a Nanopasture (for a total of 7) your bigger cities will run out of scientist slots pretty quickly.
And tbh I am not really sure why you would ever build Domes. Imho they are a bottom tier improvement. If anything a Purity player would rather skip Biowells to get his super farms running.