Long bed all the way, for me. Looks better in terms of proportions. Smoother ride. Better stability when towing. Conversely, a short bed is much better for off-roading, so it really depends on what you're doing with your truck.
I'll be mostly highway driving, hauling random junk and yard debris (like long branches, so the more space in the bed, the better), almost never have to parallel park, and don't currently have a garage big enough to put even a short bed in (our current one doesn't even fit my JGC, too tall). So, easy choice for me.
Only negative is a larger turning radius, but it was gonna be a jump from my JGC to a truck regardless so what's a few more feet?