As already mentioned, quite a few positives. Love our FWC. You couldn't wipe the grin off my face the first time it was raining/snowing/sleeting out and I reached down to turn the furnace up a bit. On more then a few occasions I've slept through night time snow storms none the wiser and woken up with a few inches on the ground. I haven't slept in a flip-pac but I knew in a tent I'd be pretty aware when the snow started building up. They really do excel in foul weather camping, or when the bugs are nasty and you are looking for a place to be "inside".
I don't get too crazy when "off roading" but I've gotten my Tacoma with a FWC everywhere I've wanted to go. Death Valley, Colorado passes, Alaska, I've been to lots of places and have always been impressed.
That being said, one of the downsides probably often overlooked is MPG. I imagine a truck with a flip pac will get significantly better MPGs, and handle the highway better as well. I can't speak to putting it on a larger truck, but I know it's there on my Tacoma. I'm not setting any speed records on the highway, and cross winds become a real pain. On trips where there will be more highway driving then actual camping/exploring, the FWC sometimes gets left behind in favor of the faster/lighter approach.
As mentioned, storing it is a small pain. If you have lots of room its not a huge deal, as you can leave it jacked up on sawhorses and then loading it becomes a few minute deal. I don't currently have lots of room, so have to jack it down to a rolling dolly and push it into my garage for storage. Adds prob 30-45 minutes to the process. I can usually get it from stored on dolly in garage to trip ready tied down inside truck bed in about an hour, working solo and having to move the other garage inhabitants (motorcycles, mowers, bikes, everything else that ends up tossed in there) out of the way. It's the jacking it up the 3-4 feet to load it that takes the longest.