Jerusalem... I can't even begin to wonder. This is one of those places where you have a great potential to piss off your friends if you're not all on the same page. How a GM treats this city would communicate a lot about the GM. It's all dependent on exactly what they did to explain it. It could reflect a dim view of humanity or a hope that that situation could turn out alright someday. IT all depends.
I think it could go one of 3 general ways:
The first way Dresden Files Jerusalem could go would be that the magical world is in chaos there, with the magical world barely able to keep up. You think a suicide bomber is a b***h, try his his ghost. That, and the psychic energy from all of the fear, hate and anger around the whole region would only spur the other magical force in the region, Faith. I'd be surprised if the Temple of Solomon didn't disintegrate any vampire or other ghoulie that set foot in it. Not to mention, Fundamentalists are scary enough, now think about Fundamentalist Wizards with Thaumaturgy....
This route of it as a hotspot could go further in one way with the Angels of the region are still crusading in a part of the Nevernever reflective of Dante's Divine Comedy, Hellgate London, Diablo and Little Nicky...j/k. But, it could also be a hotspot if it was interpreted as a city abandoned by the magical world and by the gods, but that is just one possible interpretation.
The second way Jerusalem could go is a common technique in the Dresden Files, Playing against type. Jerusalem is a center of politics in our world, in the Magical one, "Meh..." It could be a magically dead zone because of all the Faith magic combined with all of the emotions. That route would be a downer though.
The third way is actually logical. Jerusalem actually would probably be a better candidate for a Magical Casablanca/Berlin than a podunk town since the political sturggles could hide anything in it. Jerusalem as Accorded Neutral Ground would be fun because of the reasons you play a city like that, it's factioned. A main reason it could be accorded neutral territory is because there's so much magic in it. If you wanted to take it further, have magic banned within city limits under penalty of death because drawing from it is like having infinite supply of uranium bullets that explode. When something magical does go down in Magical Jerusalem, it's big.
I personally wouldn't run a game here (Not my kind of place and I don't know my way around) but if I did visit ingame, mine would be a mixture of all of these places.
That being said, I wonder about 2 other cities: Vactian City and Mecca...