They've talked about this happening in the "2050" era, which is a little earlier in the shadowrun timeline
Chicago, for example, isn't overrun with bug spirits yet
Do you remember when/where they said that?
I went looking for information on possible second cities and I remembered them mentioning a timeframe for the game, but I couldn't find it anymore.
2050 era problably means 2nd edition Shadowrun lore. Which as far as I can see runs from 2053-2059. (http://en.wikipedia.org/wiki/List_of_Shadowrun_books#Sourcebooks)
The discovery of the insect spirits behind the Universal Brotherhood happens in 2055, which leads among other things, to Chicago being put in a quarantine and Berlin being invaded by the big corporations, who divide the city between themselves and only the walled of east of Berlin remains anarchistic.
The quarantine of Chicago ends in 2058 after the use of a biological weapon and Berlin is reunited in 2072 after the corporations took over East Berlin.
So if they set the game at the end of the "2050" era they could have the second city being a freshly "cleaned up" Chicago with the former Containment Zone being extremely dangerous to anything magical, or in the divided Berlin with each district under control of a different multinational and an anarchistic east, that walled itself of.
The third place Jordan Weisman mentioned by name is Tir Tairngire, which is a isolationist elven state in what used to be Oregon, ruled by a Council of Princes. After 2057 when the Council closed the state's borders, it became rife with internal strife. The worsening economy and police-state methods of the Council ultimately lead to a successful revolution 2064.
Does anyone know of good online resources for Shadowrun? So far I've only stumbled opon this English wiki
http://shadowrun.wikia.com/wiki/Main_Page
and these two German ones.
http://www.shadowhelix.de/Hauptseite
http://www.shadowiki.de/Hauptseite