But please let me know if there are other issues I should be checking out.
There was a discussion on the forums not too long ago about the starting positions of the races in the galaxy when playing with fewer than the recommended number. For example, in a huge galaxy with tight clusters and 6 AI opponents, I was pretty consistently seeing 2 to 4 AI opponent's home worlds in the same cluster where I started, with completely empty clusters on the other side of the map. Someone, and I apologize for forgetting who, made these changes to GalCiv2MapDefs.xml:
and that nicely spread the AIs out across all clusters.
Is that something you might consider changing? I have to admit I don't know the ramifications it might have for games with large numbers of home worlds.