It really depends on what YOU will be carrying in the truck bed.
I've had both; my previous truck was a short bed with a cab-height shell. I loved it.
My current truck is a long bed with a hard one piece tonneau (with electric lock tied in to the doors), and I pretty much hate it.
My generator barely fits under the tonneau, which is fine, but I'm on my hands/knees to get anything from the front of the bed, can't carry anything taller than the bed sides without removing the cover or hauling it on a trailer, it's generally a pain in the butt. It looks nice though.
I'm keeping an eye out for a good deal on a shell and selling this tonneau because it is what I need. I will say that the electric lock on it is a must have!