Extra cities add extra complications and state management. This isn't necessarily a bad thing, but the complications aren't easily apparent and the state management feels like a lot of work.
The rest of this post ended up being less organised and more braindump than I intended, although I tried to give "information" and "navigation" each their own paragraph. I hope there's at least one useful idea buried in all the words. :-)
In AI War, individual planets don't generally have very much going on that you need to worry about except for construction (which you set up and then leave to do its thing) and enemy action (which you can follow on the galaxy map). While I haven't played much with multiple cities in SBR (and that was pre-II), my difficulties were mostly around visibility and having to manually track potential problems in each city by switching between them and inspecting a bunch of information from different places. I kept trying to hit "tab" to get to the galaxy map equivalent (and that's how I discovered that there was an underground).
I think what we need is a good overview of all the important information everywhere with an easy way to bounce between that and the places we need to go to get more detailed information or make changes. The city management screen isn't very good at this, and I haven't really had much incentive to look at the list-of-all-cities whose name I can't remember offhand. Now that I've spent some time solidifying my thinking, I find myself wanting a "war room map" view of the world that eliminates irrelevant information (like terrain, most building types, etc.) and gives me overlays and icons appropriate for the mode I'm looking at -- pollution/cleanup in one mode, crime in another, friend/foe-tagged military in a third, etc. -- that I can use like the galaxy map in AI War.
AI War's planet/galaxy split works well for getting to the right place quickly because each planet is self-contained and it's easy to see which ones you need to pay attention to. SBR's single large map doesn't provide any obvious navigation points, especially with the city sprawl we've seen in the past. Maybe we need some kind of "points of interest" system that lets us quickly get to particular places we care about. Some points are obvious and already exist (Civic Centres, battle sites), some don't (as far as I know, at least -- crime hotspots, warping saucers), and some can't (that resource I want to keep an eye on while I build my way out to it). For the last, assigning locations the way control groups work in AI War would be ideal.
