I've been playing 1.2F now for a bit and found it by far the most stable and by far better balanced attempt at this game.  But There are two issues I see still related to population.

1) Population growth cap for having multiple cities is ridiculous.  This in the very least needs to be adjusted so the top X number (by size/fame) of cities are unaffected, then the next Y cities are perhaps minorly handicapped and after that everyone is crippled.  Currently you don't get any growth if you conquer the opposition cities as your # of cities swell growth drops to 0.1 per turn.  If you play on a large map you are guaranteed to have 12+ cities yourself to access the resources scattered about so I don't see this working too well.  Or perhaps I'm doing something wrong...

2) Population growth I think should be considered.  If food and population level is a 'global' resource then so should population growth.  Your entire population should be breeding at a set rate +/- from influences like your relative prestige to your enemy & allied civilizations, heroes etc.  Then the growth should reflect in some manner the total available population in all cities and be divided among all cities with available housing.  Perhaps a base growth from its own captive population +/- hero/sovereign bonuses +/- civilization prestige relative to competitor known civilizations +/- from amount of open population in available cities you control.  Perhaps if a city had sufficient prestige relative to another city then the one would trickle into the other at some defined rate (considering perhaps a # of turns required to move from place to place, could be fixed # or based on distance from one to the other).

Cheers guys.