My dogs are barkin' !!
I think its the feet and not the shoes. Perhaps you could approach the problem from a different angle. Maybe you could toughen your feet through training. If this were the first day of bootcamp and you got your new issue boots your feet would be hurting pretty bad. But after 3-4 weeks your boots would fit your feet like a glove. Or, if you were a begginer rock climber your feet would be in big trouble. But after some time in the shoes you would be like most climbers and start buying tighter shoes and enduring more pain. Point is - shoes are made to fit a wide range - getting that custom fit right off the shelf is not possible for all foot types. Training the feet to make them tougher is an option that could help alleviate some discomfort. You might consult a pediatrist for some techniques and cautions.
I have also noticed that if I wear the same shoe type everyday it helps. I used to wear Asolo boots at work and hiking. I would wear them if I went out to dinner of to a movie (rare). I also wore a pair to hike in. My feet were fine. Now I hate those boots - and I just got a new pair before I got good advice from this board and started wearing running shoes. Hardrocks. Now I wear running shoes everywhere.