For What It's Worth:
I assume you're talking about the difference between a J-shaped stacked humbucker as opposed to the typcial single coil J pup - since you're stuck with your the routing configuration - unless you plan on routing.
If you get 4 wire humbuckers you can split coils and get a broand range of sounds with a simple DPDT switch. At least I did with a pair of Bart BB4C's. They're EMG shaped soaps and not J's so I'd imagine the variation in tone would be greater since you're covering different areas of string. Never done it with a stacked J but would imagine you be stuck with more J - like tones, as opposed to the typical fatter soap humbucking sound. I personally haven't got much tonal variation using single coil J pairs, which is not to say I haven't gotten some good useful tones out of them. But I'd stay away from single coil J's unless you like a J sound. Stacked HB's wired in series will give you a J-like tone but definetly fatter/darker as a rule - depending on the pups, bass, rigging, etc.