I think advanced refining and organic facilities are way too costly.
Refining Center:
cost : 10k M, 60k O and 40k R
produce: 100+50 M, 25 O and 200+300 R (second term is from sun)
Normal City:
cost : 10k M, 30k O and 25 R
produce: 150+150 M, 75+75 O and 100 R
Imagine extreme case: I colonise a planet with 100%M, ZERO% O and 100% R.
RC will give me 675 in total, city gives 475.
difference - 200 per month.
Now cost: 110k for RC 55 for city.
55k:200 = 275 turns before RC breaks even !!!
Not to mention construction time - I can construct 2 cities for the time AND cost of 1 RC.
It would definetly outperform RC even if I'll need to trade resources.
Yes, I understand RC may be usefull if I'm desparate for radioactives but that is not very common situation and then I would probably find faster solution then invest so heavily into RC.
Similar situation with agrarian ecosystem, IMHO.
I build few such facilities but only because I like the look
and have a lot of spare materials.
I suggest make them cheaper. 10,40,30 for RC and
10,30,40 for AE.
Lesser buildings would need rebalancing as well.
Just MHO.