I think the idea of 2 golden ages isn't bad. One (less powerful) could be trigerd by UU and the other one (more powerful) by wonder.
The first one, trigerd by UU, should be more military based. It could give your units a temporal moral boost, or maybe even upgrade their level, or lower the building time.
The other one should be more economy/sience oriented, similar to the GA we already have.
I liked the idea of dark ages too. I think there should be diffrent kinds of them.
E.g. if you lost a city to ai, and you are the one who started the war, you units will enter the dark age and will gain no moral upgrades for 10+ turns. Yours existing army could "brake" apart into several units, and you would loose your leader.
Or you could enter a (plague)dark age, if many of your cities are on "disies" terain (jungle/flood plains). Plague could brake in your empire, making all your cities loose some population (not too many, just 1 or 2).