If you see the logic in the post Barefoot, yet in shoes but are baffled by how flat shoes, including the very fashionable ballerinas, feel uncomfortable, you may want to consider what this discomfort really originates in.
The narrow toe box of a standard shoe doesn’t let your toes splay freely, which shifts your natural balance and makes your muscles, tendons, ligaments and joints either under- or overwork in order to maintain this corrupted balance. That state is not only unnatural but also one that requires enormous extra effort, and will almost inevitably lead to some kind of external compensation, i.e. artificial support. Unfortunately, each intervention into the natural functionality of our bodies tends to lead over time to further, even more serious interventions, often creating a vicious circle.
On top of that, in case the soles of your shoes are not thin and flexible enough, you lose ground feel, and with it the rich source of information that is the basis of the normal functioning of your feet. With your big toe pushed inwards, neither can you roll and push yourself off the ground with each step as you should.
Therefore, a flat sole cannot account for the natural comfort of a shoe all by itself.
However, if you tried on a shoe that is not only flat but meeting all other requirements of barefoot footwear and thus providing your feet with almost as much comfort and freedom as being barefoot does, your impressions might be completely different. Have you ever? How would you otherwise know if your feet are reacting to the flatness of the sole or to other, limiting and unnatural features of the shoe?
Thanks to the unbelievable adaptivity of our bodies (and minds) every single part of us learns to live by the standards we grow up with. Our calf muscles, for instance, shorten by up to a few cm-s from the constant ’slope’ mode heeled shoes keep our legs in. The pelvis drops forward, the back stoops, and we avoid falling by developing an ’S’ form in our spine. I, the person may not notice all that on the surface, because my body, this superintelligent machine, automatically takes care of my survival, ensuring at all cost that I don’t fall on my face and that I can still walk, run and jump.
The longer time you spend in an unnatural state, the more your body gets used to it. Realigning may take time, too! Don’t be surprised if you need to do more than simply press the reset button. Some people can only venture back to their natural ways slowly and gradually, others may be beyond the stage where a full return is still possible. Just like all bodies are different, all transitions are different, too. What you need to do is listen closely to your body, it will always indicate what it needs and how much it can take. Be wise, don’t force anything, because if you do, you may end up with an injury.
TDL Alma Libre 
Gabor 
neutral position 
‘downhill’ position
Those in need of a compromise, either temporarily or in the long run, may opt for barefoot shoes with an insole. Take care of your needs, whatever they are! Some manufacturers offer their shoes with soles of variable stack heights, The Drifter Leather, for instance, can make your shoes with a sole of either 4 or 6 mm, with or without an additional 1 mm cushioning. Ahinsashoes put very thin soles on all their models, but they let you choose between a 2 mm barefoot insole or the so called ’comfort’ one that has a 4 mm cushion under the heel.