I see where you are coming from on the able to put it back to stock easily, but then again this isn't a brand new lease vehicle, so i wasn't as worried about it. As for the roof mount, i wasn't suggesting that as much as throwing out another idea just to get people to think outside of the box a bit. I mean everywhere has advantages and disadvantage:
Under the front seat: nice and out of the way, only speaker leads to unhook if you want to remove the subs for full hauling ability. The down side is the water damage possibility i don't think i've ever pulled an amp that was under a seat for a long period that didn't have at least some rust on it. We shoes, details, and the fac that most people just run self tapping screws through the floor giving a way for moisture to come in.
The back of the seats is good, and out of the way unless you want to use full cargo space, and again is pretty noticeable when removed to change amps, or for vehicle resale.
On the Box makes 100% removal easier, but you have more wires to unhook to do so, and again makes 100% removal really easier for a theif w/ a good pair of cutters. and again most amp manufactures recommend against this.
and of course most of the other things are more work for the install. this is the category that i usually fall into because a basic install is just boring to me. I feel, if you spend the time to do something, make it cool. You don't have to pay someone to do it for you, just get an idea of where you want it and start working out how to do it, if you get stuck ask for some more opinions. Even if you don't get stuck, post your idea before you start, i'm sure a few people here will give you some ideas of potential problems.