The two things I've noticed are significant tightening in my lower back and discomfort leading to pain in my heels. If I stand barefoot for much of the day, the heel pain can be so bad that there's a sort of burning sensation as I lay in bed at night.
Wearing comfortable, supportive shoes has greatly reduced the heel pain. You could counter that I simply need to spend more time on my feet to condition myself, but as I saw no improvement in the pain over the course of weeks, I'll be disinclined to believe you. :-)
My dad used to have knee issues like crazy. He now moved to a village and never wears shoes. All his knee issues are gone. Better yet he can run into a river as if it was a paved road. (Riverbeds are covered in small slippery rocks which make it very hard to walk on)
Also you probably have some kind of problem with the fascia at the bottom of your foot. Get a tennis ball and use it to massage your whole foot. Do it once a day.
It will hurt like hell to start but your feet will feel awesome after it. After a few weeks the initial pain will go away completely.
My point in posting my experience is that everyone is different, and people who say, "just do X and it will solve all your problems," have very little likelihood of being accurate. I'm glad your father is doing well, but trust me, I have a host of unavoidable, congenital issues that I have to deal with. Many, many people have other sorts of congenital issues which will make going barefoot painful.
you probably have some kind of problem with the fascia at the bottom of your foot
Nope. The pain is primarily around the edge of the heel. It's hard to explain, but definitely not tendon or ligament pain.
True if you have congenital issues eg: flat-footedness then you'd need to get special shoes with support built in.