Now, I do have quite a few cardboard boxes, and they never feel ideal to keep everything together. The more popular the game, the more wear and tear I'm naturally putting on the box, and if i keep the game and manual seperate from the box, then I just have a bunch of empty boxes sitting around taking up space. The only cardboard boxes that I do find tolerable are the Accolade ones, and that's because they're sturdier and much easier to keep in nice shape.
Maybe it's just me, but I guess I'm not anal enough to prefer the cardboard boxes over the clamshells. Even if it does take away that "original box" factor, I would easily trade in the cardboard boxes for clamshells with some nice alternative art attached.