Hong kong definately had the most interesting fluff in SR3/4. Berlin was pretty much relegated to "Oh, there's anarchists. And Lofwyr."
So you're familiar with the PnP? Could you go into a bit of detail with each of the cities and explain what you like/dislike about them?
I played some 2nd, 3rd and 4th edition. It's been a while though since the people I used to GM 4E for all got hooked on burning wheel and kinda dragged me along with them. Off the top of my head:
Berlin: Germany pretty much got taken over by Lofwyr, one of the great dragons, and his megacorporation Saeder-Krupp to a point where "Germany", "Lofwyr" and "Saeder-Krupp" could be used pretty much interchangably. The city didn't really appeal all that much to us and we never bothered with it in my local PnP groups except for a one-shot where we tried to steal the crystal bequeathed to Lofwyr in Dunkelzahns will. (We all died horribly). Most of the background marterial written for Berlin is in shadows of Europe, though snippets exist whenever Lofwyr is mentioned too. It's not really compelling as a runner location since most of the fun in Shadowrun is the squabbling between dozens of factions and Berlin is basically smack in the backyard of a monolithic megacorporation HQ.
Chicago: Was the focal point of a badass series of adventures centered around the Universal Brotherhood (you can find PDFs if paper copies are too hard to track down). Long story short, UB posed as some sort of new-age scientology slash humanitarian place where people came and became happy again. Truth was they were a front for a giant hive of insect spirits who needed human hosts to posess to exist int he real world. Things rapidly went south, the city became quarantined and eventually Ares megacorp detonated a tactical nuke in the middle of the city to take out the hive. Serious wasteland potential here. A lot of background material was written for Chicago, including a full sourcebook as far as I recall.
Denver: When the world turned magic again a bunch of factions rose up which fragmented the ol' US of A. In the north you got UCAS (United american-Canadian Somethingorother), in the south you got NAN (Native American Nations), there's Tir Taingire the faggot elf sanctuary in what used to be California etc. Once the dust settled and the various north american nations had to learn to live with each other, the borders were established and a treaty was signed in Denver. Ad part of the treaty, each of the various factions got a share of Denver as the Treaty City. Since noone realyl trusted the other nations and everyone had seperate ideas on what was legal and what was not, each faction walled off their respective part of Denver turning it into a smuglers paradise. It's also the home of the Nexus, which is the most (in)famous data haven, home to Cap'n Chaos and co. (Think a baddasser version of The Pirate Bay for shadowrunners). There was a long ongiong living campaign centered around Denver (you can find the adventures circularing online in PDF format) that was pretty well written and saw players balancing reputation between a dozen different factions. Like chicago, a decent amount of background material exists for Denver.
Hong Kong:The entire city is built around a leyline nexus and the locals are bigtime into feng shui. A large section of the 4E sourcebook "Runner Havens" is dedicated to hong kong. It's basically like a less faggy neo-Tokyo with all the megacorps and several AA's staking out their claims and a couple of dragons lurking around in the surrounding countryside. I ran a homemade asia campaign out of hong kong that saw my players playing ninja intereor redecorators to disrupt leylines which ultimately resulted in a bunch of toxic spirits being loosed and a 4-way battle around a giant cable car hauling people from the main island to the residential complexes and temples in the mountains on the mainland. Ah, good times. Hong kong is more neon blade runner slash oriental cliche than Seattle, so it'd definately necessitate a new tileset. Berlin could get away with copypastaing the Seattle one, Chicago is basically a nuked seattle and Denver is Seattle with walls.
London: The only source material I know of for London is the 3E Shadows of Europe supplement but I'm pretty certain there's more than that. We never went there in the campaigns I played (closest we got was Tir na nOg, Ireland turned faggy elf sanctuary). The main interesting feature with London is that the famous smog is back with a venegance. Toxic fog turned much of London uninhabitable and large parts of the city has been moved into an extensive underground network inspired by their subway. London (and britain in general) is also frequently mentioned as the breeding ground for magic cabal conspiracies linking back to the Earthdawn campaign setting. A monocle city to be sure.
If I were to have my way, the city preference would be
Copenhagen (See Crash 2.0/Winternight/Shadows of Europe) > Hong Kong > London > One of the faggy elf nations (Tir Taingire) > Chicago > Denver > More seattle > Berlin