The problem with padding is that humans actually already have an extremely sophisticated active shock and balance system in our ankles and knees, and when you add a passive system like padding on the feet, you force that system to work harder and adjust in unnatural ways. Essentially, you're setting yourself up to always be walking on unsteady ground.
So you might want to first try going barefoot for a while, and see if that helps. If you aren't accustomed to standing barefoot for long periods, it will take some time for your body to adjust, but I suspect that you will adjust faster to that than to padding.