I've thought about this too.
Short bed pros:
easier to park
seem more desirable when restored
better breakover angle for off-roading
looks taller with less lift (my opinion)
easier to find other bed parts for (toppers, tonneau covers, etc.)
Long bed pros:
more hauling space
more load capacity (w/ Metric Ton package)
better ride because of longer wheel base (in theory, cannot confirm or deny this)
Short bed cons:
No Metric Ton
Stiffer ride?
slightly less bed space
pricier when you find a nice one
Long bed cons:
longer (harder to park)
worse breakover angle
harder to find other bed parts (toppers, tonneau covers, etc.)
It all depends on what you use the truck for. Honestly, the short bed has been fine for everything that I've needed it for, I have hauled kayaks with it, I just needed to strap them down, which you should do either way. The only reason I have to want a long bed is because of the metric ton package, which was still an option.