I have a 2004 Super Duty with a 2006 A.R.E. Z-series shell on it. It uses the old style C-clamps to mount it and does not have the electric lock on the door, but it can be added as an option. It does have the gray carpeted interior and the front tilt down window for cleaning. It also slides open in the middle in case you have a sliding back window in your truck, which I do not. The side windows open slightly in the rear, but that's all. I bought this vehicle used and the shell was already on it, however it has been one of the best shells I have ever owned, and I've had a bunch of them!
Post #4 and #5 pretty well covered all the good stuff to get, but there is one more thing I wish I had on mine. I'm converting an ambulance for camping now, so I don't sleep in the back of mine anymore, although that used to be my preferred method. Having side windows that open is almost mandatory for sleeping in the rear, however mine only swing out about 3" with the hinge being vertical, more like the rear seat vent window on my truck.
Once you put a shell or topper on a truck, accessing things in the front of the bed become a real pain in the butt. I have a Drawer System in mine right now, but that only solves a few problems, and creates a new set of it's own. So, I wish I had full length side windows that would open by swinging upwards like the rear door does. Then I could run full length side boxes that sit on top of the wheel wells, and are accessed from the top to keep all my tools, recovery gear, emergencies supplies, etc. in. The full width and length of the bed, along with the full height of the shell (with the drawer unit removed) would then be available for use.
Update: Apparently poster #6 posted while I was writing this. It also looks like he has the same idea about the side windows that I do. Isn't is amazing how great minds thing alike!