A place where there might be room for significant improvement in the performance is the barbarian turn. It seems to take extremely long. I'm in the digital era and the entire map is settled, I doubt if there is even a barbarian unit to be found anywhere on the map, but the barbarian turn still takes 3-4 times as long as all the npc player turns put together...
This is a problem with the DLL. I can't help you with that... maybe FiresForever or chrome-rome can. Some features I listed (multimaps, underwater cities) require DLL, but I am thinking that someone who knows better can help us. A general improvement in the AI would also be a part of any mod as large as mine.