Well, I'll chime in on this one. I have an ARE MX series cap on my truck and I love it. I've slept in the back of my truck several times, even thru some pretty harsh thunder storms. Comfy as can be. Well as comfy as you can be with high winds, blowing rain, lightening flashing and thunder clapping. lol
My set up is a metal rack I designed that, slides in and out of the back so I can store my gear below in boxes (I store everything in Rubbermaid Action Packers) and sleep on top. The bed is almost the size of a standard queen sized bed, and that is due to the foam mattress, there is room on the sides for storage of clothing etc. When I get home everything comes out to make the truck more useful for hauling other crap.
I have the small crank out vent windows and the drop down window in the front with a vent window in it as well. On all but the worst rainy nights I can open the drop down window, and if it's not raining I can open the crank out windows or prop open the back window a bit for a nice breeze. Also, I have experienced the leaky windows that most people complain about. But I have found that if I lub the window seals with some vaseline it keeps the seals in good shape and they seal up well. For security/privacy I've got covers that velcro over the window frames on the inside. These are home made, thanks mom!
I have also designed a nice rack that will go over the top of the cap so I can carry my kayak, ski's and other stuff up top. Similar to a ladder rack, just that its smaller and conforms to my shell. Just need to get back to work so I can afford to make it.
As far as removing my shell I've only done it once and my 73 year old dad and I did it without a problem. It only weighs 190 lbs. And, if I had to take it on and off more often I would get something like this set up.
http://www.jedi.com/obiwan/jeep/pics/ratchet_hoist15_720.jpg
My shell has never moved on me, but my dad's has and we just drilled a hole thru the shell, and the bed rail of the truck. We dropped a bolt thru some washers we made for the top and the bottom and tightened them up. Hasn't moved since.
So, if your going to use your truck more for camping, IMO you can't beat a quality made shell. I've never used a bed cover but it just doesn't seem as useful to me. Ya still gotta remove it to haul large items. And, the idea of sleeping in a RTT in bad weather is barely above the idea of sleeping in a tent. And, sooner or later your gonna get stuck in bad weather, and I'd much rather be listening to the rain fall on the shell while resting peacefully rather than worrying about getting wet.
Sorry for the long winded response, and I hope this info helps.
