This article was mentioned in the commuter forum a couple of months back. For me, clipless is the only way to go. This is for a couple of reasons. I do pull up on the pedals, not often, just to give my quads a break. This really seems to help with fatigue.
The most important reason is because I spin and don't mash. I can't spin with flat platforms. I have arthritis in my left knee, well actually both but the left gives me the most problems. When I ride my one bike that doesn't have clipless system, the next day my knee will be in a lot of pain. If I ride only a short distance, say a mile or so, I am fine. Anything over that and I will be hurting the next day.
I like the idea of using any shoe, but in my case, it really isn't possible. I was thinking about getting some Powergrips. This might help.