It seems to me that the game is balanced for smaller maps.  This balance breaks down fairly quickly on the larger maps and does not scale at all into the insane or super large maps.

First things first.  1 pop = 1 production.        This should be true only for the Capitol planets or with Civ Unique or Galaxy unique improvements.     Or perhaps something that can be purchased as a racial trait.

Otherwise I think there should be a scaling drop off in production as population increases.

Pop 1 to 8         1 to 1
Pop 8.1 to 12     80% efficiant,  then 70%  then 60%  then 50%   as population increases...   or make it scale so that you always get 1 to 1 for first 8 pop but then the additional pop is less and less and less and less efficient.  

Perhaps efficiency centers can be built that increases the efficiency of the population, but as population increases the infrastructure to support it automatically increases so the population should become less efficient.

Make Happiness/morale more damaging/important.     Give bigger benifits for having happy people, and much more drastic impacts to having unhappy people.  
Other games have riots, or strikes or shutdowns....  perhaps total production needs to be impacted severely by having unhappy people.

Change the large empire penalty from a static moral hit to a scaling income or income and moral  hit that scales with the map size.    If I am on a small map with 20 planets that is a totally different game than an immense map with 2000 planets    The thresholds of when your empire is large should scale.  My thought is that is should ALWAYS be based on math such as this:  Number of Planets in My empire /Number of Planets I am ABLE to Habitat in Galaxy.   Anything over .10 should be large at the beginning of the game...   give us techs that offset this so that by the end of the game we are looking at .50 or .75 before it hits.


My point is when playing on smaller maps with fewer AI players the game is actually surprisingly balanced.

It just utterly fails at the things is SHOULD be best at and are the focus and bragging rights of the whole 64bit move.... HUGE maps with HUGE numbers of opponents.