The rifle shoots a light weight bullet at high velocity, which creates alot of hydrostatic shock which ruins alot of meat around the bullet placement.
The shotgun shoots a heavy weight bullet at a low velocity, which does not create as much shock, which saves more meat.
Oh come on, you can do better than that!
Shot placement, shot placement, shot placement!! If you hit 'em where you should (in my opinion) hit 'em - in the ribs and thru the lungs, no meat is damaged regardless of rifle/shotgun choice. Not only that, but I would also argue that you're much more likely to hit them where you should if you're using a rifle instead of a shotgun. Greater accuracy of the "tool" added to less likelihood of a punch induced flinch equals better shot placement.
Now, there ARE occasions when the deer doesn't cooperate and you can't get a nice broadside shot. It's either quartering to or away, etc. In those cases (which aren't that common in my experience...you can almost always wait for a broadside shot) you are going to ruin some meat, so MAYBE you could argue that a shotgun will ruin less. I say it doesn't happen often and there's very little additional meat damage. Not enough to offset the advantages of a rifle.
As for your second argument - that you "guess" more rifle-hit deer are lost than shotgun hit deer - that's a very difficult theory to test. I would "guess" that at equal distances, more shotgun deer are lost than rifle deer are. Why? Reduced accuracy/poor shot placement.
Hunters are possibly more likely to take a longer shot with a rifle than with a shotgun and may very well overestimate their ability to successfully make such a shot. That overestimation would cause a poor shot at distance with a rifle, a shot that may not be taken at all with a shotgun. That, however, is not the "tool's" fault, at least not the tool we're discussing. It's the "other" tool at fault in that case - the hunter.
OK, I've completely taken this thread in another direction. I'm sorry. This is an interesting (to me) discussion, however. I primarily hunt in shotgun only counties of NY state and have taken all but 2 deer with my shotgun. One was with a rifle and one with a muzzleloader. But I'm very much looking forward to those counties switching to allow rifles. When they do, I'm switching to my 7-08 as my gun of choice. It is bolt action and my shotgun is semi-auto (reduced recoil, of course!) so the shotgun has a slight edge there, but follow-up shots are rarely needed anyway.
I may change my mind after using the rifle for a while (if the option ever comes to pass,) but for now it seems to easily be the best tool in my gun cabinet.
Zhe Wiz