Well after 30+ years of commuting, touring, etc. I find the balls of my feet are numb. After a few years of numbness the Dr. said the feeling would come back if I didn't ride for a month or so. That was true, but as soon as I rode again the numbness returned. Now it won't leave at all. I wear Specialized Sonoma shoes and use Phil FLAT PLATFORM CHP pedals. They are the best combination! The Phil pedals allow any footwear to be worn without discomfort or pain. I also use Specialized track pedals on another bike and find the Sonoma shoes are necessary for comfort.
I use clips consistently, and find a "boost of power" when intentionally pedaling in a powered circular motion, definitely using the clips to advantage.
Most important to me is a firm yet resilient saddle. I have an Ideale 90 that fits like a glove, but only on my fair weather bike. The rain in the Seattle winter and sweat in the summer on long trips softens and stretches leather saddles. My solution is the Avocet Touring II (off topic). Minimal padding (5mm) and just enough resilience for comfort on LOONNGGG tours.
Markku Klubb
Seattle, Wa USA