Actually, not usually, no. I wear carbon soled shoes because they are the stiffest and I have bad feet. For me, even with clipless and cycling shoes, I was having trouble. If I'm riding distance, then I need super stiff shoes.
In your case (and for most normal people), carbon isn't necessary for comfort. A normal bike shoe with a stiff sole will work wonders, so when you go to clipless and get the shoes that work with them, you'll be fine.
In the meantime, you could try finding some shoes that are stiffer to use with your flat pedals. I know that some people actually ride in hiking boots in the winter (with flat pedals) for the warmth and the stiffer sole. You could also get a pair of mountain biking shoes and wear them without cleats on your flat pedals too. Then when you go clipless, you'll already be used to the shoes (and you can just add cleats to the mountain bike shoe). Or - find the newest, stiffest pair of athletic shoes you own and use those for now.




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