I play 'semi-friendly' MP a lot with my friends online and we like to build up to at least the late Renaissance or Industrial era before we wage our epic battles. We play Continents, Standard size map, on Epic speed with default AIs to fill in the other slots. As a result our games tend to drag on for a long time and the turn transitions become unbearable in the late game.
Recently we have been taking City States out of the game entirely and leaving the 'major' Civ team count on default. It certainly feels like the performance is much improved without all the CS AIs bogging things down. So long as you don't mind leaving Greece or Siam with a handicap and ignore the Patronage tree altogether, it's actually quite enjoyable in my opinion. City placement is much better without a CS in the way and it's more difficult to gain a foothold on another continent since you can't just bribe a CS to let you in their land and assist in harassing your enemy. Try putting the CS count to 0 and see how much of an impact it makes for your games.