Why even use factories and labs at all? To win, all you need are farms, cities, and stadiums. Grow your population and win. Factories/labs are never worth it. Never. The capital buildings (mfg cap/research cap/financial cap) are good, but the base improvement buildings are just never worth it. To get a planet up and running, space elevators can be worth it, at least temporarily.
Well, I have never tried that and I don't quite agree with you since Xeon factory for example gives 30% production so you can take the advantage of two factories in each system which is at least 60% plus production only for two tiles. Each city requires two farm and one entertainment center to grant a population of 4. That almost add 100% to your production. With four tiles you can have four Xeon factory which gives you at least 120% extra production so to me factories are interesting option if upgrading was not so expensive ( this means that the game is unbalanced, there is no need for factory).
I have no idea where you're getting this math. First of all, forget farms on production planets. One high class planet can provide enough food for about 10 planets, if you use farmers and have monsantum. So in a 20 planet empire you only need 2 planets for food, maybe 3 at the most and 2 of those can be garbage class 6 planets.
As for the production planet itself, sure factories get adjacency bonuses, BUT SO DO CITIES!!!!
I just finished a game where I had a class 20 precursor prison planet, and it was generating 2.2K military production per turn by the end of the game. How? I got it's population up to 140!! How? I just placed a bunch of cities together, with a megalopolis, and a colonial hospital. Each city only gives a base +3 to population cap, but I got that planet up to 140 pop. That's because while I may have had only 9 or 10 cities on the planet, their adjacency bonuses increased the population cap by... I guess 3 or 4 fold. I also had a precursor factory on the planet and of course it had inherent production bonuses and I had leaders and manufacturing relics. Anyway, point is, that planet had cities, stadiums, and a couple of special buildings. Not one factory! Not one!
And then I had a research focused planet. That planet had my research capital and temple of enlightment. The rest of the tiles were cities and a few stadiums.
As it is right now, this game's infrastructure is totally and utterly unbalanced. Factories/labs/markets need a big buff, and cities need a big nerf. I suppose the most basic way to nerf cities would be to drastically increase their food requirement (like a factor of 2 to 4). Improvement buildings really need to be buffed. I seem to remember in GC2, even the most basic market gave you a 25% boost to income, whereas in GC3 the first buildings give only 5%, maybe up to 10% if you get lucky with adjacency. That should be increased.
Another possible way to handle this is make morale more punishing, as others have suggested. Synthetics would need to be balanced around that as well.
But yeah, as the game currently stands, it is absolutely stupid to ever build a single market/factory/lab. Never, ever, ever, ever, ever do it. Ever. (synthetics are an exception).