There are many reasons why NOT to take an automail:
Pain- I have lost two of my teeth and I had enough pain when they were being treated. I am fearing the day I get porcelain teeth to replace the stumps I have now.
Undergoing an automail surgery, you would get no pain medication during attaching of the nerves and rehabitation takes years, continuing with even more pain in rainy days.
Heavy- With a heavy weight hanging on your body, your skin and muscles undergo a lot of stress. It requires very good physique yo be able to move
Unpractical- May rust when in contact with water, needs oiling and oil smells, you can't feel with automail, and again, it'll take years to learn to move it
But I would take an automail if I lost a limb since the other kind of replacements presented in FMA seem very weak and easy to break. I think automail is for adults only since kids still have some growing to do, resulting in automail needing to be reattached every couple of years.
This is a tough one: Years of pain but permanent help vs Painfree life but weaker prothesis?