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-had to undergo very painful and lengthy surgery to get automail 

-had to relearn how to write because of his prosthesis (there’s a post going around showing he had to switch hands etc) and his handwriting is likely a lot worse due to that. This means automail isn’t super good for delicate work, unsurprising, considering what it’s made of. 

-experiences phantom limb pain and therefore other associated stuff (this was only really shown in the manga)

-cannot go anywhere too cold without changing his automail or he’ll get really bad frost bite and it will stop working

-cannot go anywhere too hot, period, because the metal attached and under his skin will overheat and he will be badly burned

-Reattachment is painful, but needs to be done frequently if he breaks or outgrows his automail

- it’s HEAVY so much so that the strain has the potential to cause stress on his body, enough that it’s even theorized as possibly stunting his growth.

-it requires really frequent maintenance or it will break down, as shown by how when he first moved out he forgot to do that and it…broke down.

-when it does need to be repaired, it takes time to do that, during which Ed uses regular prosthetics (that usually don’t quite fit him).

-costs a lot of money (not a problem for Ed due to high state alchemist salary/having mechanics as surrogate family, but explicitly noted to being the reason why most people in the fmaverse stick to regular prosthetics along with the painful surgery)

So Ed can’t actually do everything perfectly and experiences a lot of extra hassle, problems and pain people without automail don’t have to deal with!  And any advantages he does have are more suited to fighting than day to day life (being able to incorporate weapons/fake out people who want to blow up his arm).