I have tried both. I have tried removing the rubber pads from the stock foot pegs, and I have tried replacing the stock foot pegs and toe pegs with units from Knight Designs.
Removing the rubber pads does help, but the naked foot pegs feel odd under foot, and there is a bit more vibration due to the lack of rubber padding.
The Knight Designs units are very well made, and I still like to use them for longer trips, but not for commuting. They lower your feet about one inch, which is good, but you have to be careful in making left-hand turns and up-shifting at the same time (say, turning left from a stop light). It is very easy to touch the road with your left boot! Also, mine lack rubber padding, so there is a bit of vibration from that. Finally, your side stand will hit the underside of the left foot peg (and vibrate against it), and the center stand will hit your left heel (and vibrate against it).