My coworker, with a 15 mi commute, just switched to clipless for the same reason. He's in heaven, says in the 3 years he's been commuting his feet have never felt better.
Now for my new found "religion" PR (or BS, depending on your point of view) - try Vibrams! I wear my "barefoot" shoes all day everyday and my feet have never felt better. I ride in them on my trike with platform pedals and they are heaven sent for that as well. This is the opposite of Tulip's advice - let your feet work instead of stopping them from working. The VFFs will develop muscles in your feet you never knew existed and, after the original "ouch" of muscle development, your arch will be stronger for it!
Off my high-horse - either platforms or stiffer soles might help as well.