Hy Nachos,....what you're talking about is one of the things that also gets me very mad... but I'm not the one who could fix... only Firaxis could, and seen from the very little they have managed to bring us in patches up to know... it sure isn't going to happen tomorrow....
If you look at all the scenarios available, every big/good scenario has the same problem (as one can already start to notice on the WW2 scenario from Firaxis). The problem is the code for CIV3 uses exponential functions, meaning the more cities you use, the longer it takes square.... they just gave us a very crappy code!!!
The Version of the scenario that is now available is already the second version, as the first one was based on an even larger map, but had just awfull times between turns (it was a great map, 512 cities and a lot missing....). I already changed to a smaller map as it is now to make it better... removing even more cities would just make it to unrealistic.. it already hurts me to see my bith country belgium represented by so few cities....
I hope this answers your question....