I powered through the final missions of both campaigns in CivCity: Rome last night. While mostly my framerate was nice, those end missions were able to bring it down still. Most notably, I discovered that they have a serious pathing problem with their woodchoppers -- if there is no more wood available they must be doing a brute force path through the whole world every tick or something. I was getting about 5 fps on the scenario, then deleting my woodchoppers immediately brought it back up to 20-ish. Still not great, considering, but at least playable.
I guess I'm a bit biased, as we spend tons and tons of time on the Age games making sure to avoid problem cases exactly like that one. It's not rocket science, you can easily do the path checking on a delayed interval or even take into account special knowledge of the problem -- in their case, wood never comes back so you can use that data.
Anyways, with CivCity now behind me, I fired up Children of the Nile again today. I'm hopeful that this time the framerate problems I had with it before are long gone, and I'll enjoy it much more. Of course, in a few days time Saints Row will take up much of my free time...