Leather tanning methods and the quality of hides have gone downhill drastically over the last few decades. There are still some good suppliers, but they are much harder to find. Leather now is much less breathable, finished in almost a plastic like way and less flexible, the cows growth being sped up creates stretch marks and less elasticity like older skin. So, the shoes we walk in today (unless they are very high quality) will not mold to the foot in the same way. That is why straight-last shoes, with neither left nor right, were able to be used for a few hundred years, up until the mid-19th century. A few hours wear and they molded to the left/right of the wearer. Simply, their shoes were lighter, tighter, and flexed with the foot.

What this means is that the foot continues to work it's muscles. Today, with shoes that cradle the foot instead it creates muscle atrophy and flat-footedness. Lazy feet will hurt more when asked to walk in anything not super supportive. Their shoes were also better fitted. Today's market has widening feet due to a number of circumstances including weight. However, this widening only affects the joint spread of the foot, not the heel. Shoe last creators seem to ignore this and have been widening the entire last, leaving us to get blisters on the back of our heels due to ill fit and stiff leather. The quality of the standard leather shoe today just isn't meant to be an everyday shoe, so it's an impossible analogy to what was worn a hundred or more years ago.

As a reminder to commenters:

Please keep in mind that you are not a source. Just because you wear leather shoes and don't have a problem with it, that doesn't mean that saying so and leaving it at that is an answer up to the standards of /r/AskHistorians.

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The most expensive most luxurious shoes today are leather shoes. Why does OP think wearing leather shoes causes foot problems?