yeah, how about just using a mat...
as for the
deep squat v shallow squat.. my knees feel better since I switched, however I also do less running now so it is hard to say for sure whether it has anything to do with squats.
I will say though that deep squats are WAYYY harder than shallow squats, that couple of inches between just above parallel and just below parallel can mean a large difference in the weight you can lift. I think this is a big factor for most people (especially men who have more severe ego issues...not bashing men, but it is the truth)
Msg Factory it will take your knees a while to adjust to the new range of motion, but once you do I am sure it will feel just as good or better for your knees. You may have to take the weight down somewhat and build back up.