The only problem I've ever really had is foot fatigue- (no need for bicycle shorts! Brooks saddles for the win.) so I would try to wear the shoes or boots that caused the least noticeable aches. Not a perfect solution, with the result that some of my regular shoes have funny markings from the clips and pedals. Taking a break and walking always alleviates the ache, or spying a very cute pony. Luckily, these things are easy enough to do.
When I finally started taking spin classes this year, the intensity of the cycling in class with no breaks or ponies, exacerbated by standing(!) while pedalling- something that I never do on the road - made the foot problem impossible to ignore. My foot would cramp or creak very painfully in my regular running shoes.
So, I did a little research (google) and decided to find some real cycling shoes.
Yay, Bever outlet store!
I found some cycling sandals for half-off the price. Eager to test them, I wore them with socks, in public, on my ride to the lowest point in the Netherlands. The look of them, and the effect of them enabled me to ride for a few hours without wanting to take any breaks. God forbid anyone saw me like this. Oh, and my feet didn't ache at all.
FYI, I'm not getting a clipless pedal system. I don't care about efficiency/yadda yadda, only making my feet feel better and this seems to work and will ease up the wear on my regular shoes. I did buy some cleats to try on the pedals in spin class (evoking a great joke at the bicycle store about spinners falling over like dominoes when I fail to unclip properly). The clipless system in class is fun, but it's not anything I need for my bicycle trips.