Gotham City, Ma
Two cities×Two storylines equals?
Metropolis, NY
DC's decision to set its comics in a variety of geographically vague, fictional cities, as opposed to Marvel's 'The World Outside Your Window' approach has always irked me.
 So, behold my solution to what needn't be an as overly complicated/overly thought about (other than by me, obviously) issue:
Superman and Lex Luthor are what's on? It's Metropolis!
When they're off folding laundry? Welcome to New York City.
A Dark Knight, plenty of young, mostly failed sidekicks? The Joker? Harley Quinn!?
The correct answer's gonna be Gotham City.
When other, less angsty/scowly, cowly characters are the order of the day? If it's even day, for that matter? 
It's Boston, Massachuset
The same goes for San Francisco/Coastal City, California and Chicago/Central City, if for no other purpose than to get rid of all Generic Equivalentvilles at once. 
Except for Smallville, of course. You can't take Kansas' only claim to fame away!
On a similar, yet not at all the same note, with regards to other places of note:
 it's still sexily lurking. Not lost in the fucking Bermuda Triangle!
Ditto the Fortress of Solitude, which needs to be all icy and far away, else it just ain't Kosher. Not off the coast of Cuba like an all-included, 'Hedonism 2' style vacay.
Pictured, Right: Martha Kent's grain silo: Exquisite example of Art-Kryptique architecture, planted in the middle of a Kansas cornfield, because Mom.