I was told awhile back that its caused by the amount of trade routes that the computer has to deal with, and thats why it sometimes pauses for a bit when you raze a city, because it checks if any trade routes were canceled.
Through the editor you can make airports a small wonder and maybe harbours to (keep in mind that you can't have colonies if you make harbours small wonders, ran into that problem myself). I don't know if making harbours and stuff cost more would deter th AI from building them, but you could try that too.
Oh and the guy above me has good ideas to, on a earth map I set all worker actions to take three times as long as they normally should, and it worked alright, there wern't roads and other improvments on every single tile, but all the tiles in my core were completely built up and most outer cities wern't half bad either. The less roads helps cut down on improvments.