It's a fault that plagues almost all grand-scale strategy games. Because you always expand and expand and expand, you'll come to a point where you have 20 cities and can't really be bothered to check most of them out. This was mostly dealt with in Galciv2 with the specialization of planets, just have your planet full of some building and you don't need to manage it much at all after that.
Now, I don't know the scale of the game, whether you really do expand uncontrollably and end with dozens of cities or not, but there is an interesting mechanic that might be suited to deal with it.
You could use a system of "action points" where you have a certain amount of them each turn, and must carefully think where to invest them. Maybe you want to move an army? Or perhaps build something in a city? Casting a magic spell would be nice too, or engaging in diplomacy. Decisions, decisions.
This would certainly lower the amount of time spent on each turn as you can only do a certain amount of things(and especially lower the amount of time the AI thinks about it's turn, I suspect), and so your decisions would be very important, and it would somewhat "force" you to a certain style of play. (If you have huge armies, you'll be spending most of your action points in moving them, and such)
There are many disadvantages to this idea as well, especially for the people who want to tinker with everything, but I think it has enough merit to at least think about it.