As someone who's run Ptolus and Freeport campaigns under 3E, C&C and 5E, I'd choose 5E, which balances social and combat skills without requiring someone to go all-in on one or the other to make a viable character. (In 3E, even going all-in on a concept wasn't always enough to have the requisite skills -- witness all the 3E rangers who didn't know how to swim.)
Urban environments are typically not going to be ones where highly punishing rulesets, like Shadowdark and OSE rulesets, necessarily makes sense, since often "combat" will be social or political. But given that you want it to be a fantasy RPG, having a system that supports throwing down when necessary, 5E would be my choice.
That also means you can use a lot of great urban fantasy resources, like Cawood Publishing's Monsters of the City (highly recommended) or Kobold Press' Cities & Towns (if you're looking to build a city from scratch -- not a good purchase to supplement an existing detailed city, IMO). And, of course, there are tons of wonderfully detailed cities out there, if you're looking to grab one off the shelf. I first got Ptolus in 2006, and even said (maybe even on ENWorld, come to think of it), that I could easily see using it for the rest of my life. And so far, it's been a great experience and I expect to be using it for many more years to come (now with the 5E edition).