Feels like people often misunderstand Ed’s running short joke purpose & why that’s even a thing in the narrative.

On a surface level it may seem like a typical old shounen comedy trope, but it’s far from it. It’s merely a coverup that peels a lot of grounded layers to him.
Ed being short early on is a tragic and human-like assessment of his character and personality, shedding lights on his frailties and what he underwent in life. Small things bugging him is one of many insecurities he has & is completely justified given what he sacrificed.
The reason why he always hated being called short was that it implied he wasn’t good enough, not a good enough alchemist and not a good enough big brother. But when it came to Winry, the feeling was even stronger, he hated feeling that he wasn’t good enough to earn her love.
Ed had to bear a lot of burdens, notably him giving up a large chunk of his nutrients to provide for his little brother’s body for years, be weighed down by his heavy automail limbs, prioritising his brother’s body over his own through constant travel; day & night research etc.
And an unfortunate inherent distaste for minute things like milk which are essential to his physical growth.

This is why even though Ed’s short stature is used as a running joke throughout the series, it actually enhances his character & eventually, gradual change happened.
Very slowly, so slowly that you didn’t even realise, Ed got taller. Suddenly it hits you, he’s not shorter than Winry anymore. In fact, he’s taller than her by a decent amount at the end. He’s still not lanky by any means, but that extra bit of stature means everything to Edward.
This is crucial to Ed’s self-worth, and his desire for love, acknowledgement and acceptance from others. The very thing he dearly misses and was the reason he attempted to revive his dead mother back then; to experience his mother’s warmth and support once again in some fashion.
Though, through Winry, who is the closest to get to Ed to open up about anything and acts as his shoulder to cry on, he can once again experience that special and intimate bond, make him feel whole again. Without her, he would lose himself.
And there’s no telling if he can manage another failure in life, especially when its human connection & love. It’s one of the things he at the very least deserves after sacrificing his lifespan due to fatal injuries, metal limbs stagnating his growth & being so dedicated to Al.
Not to mention the general human insecurities that hindered his early years, which further makes his late and steady growth all the more satisfying.
He was just a kid yet suffered so much just for wanting to see his mother’s smile again and experience her warmth once more.
He usually hides behind his own fake smile to cover up the pain he feels. It’s always the broken ones that camouflage behind a smile, it’s easier to hide the hurt and emptiness to smile instead of cry.
It only makes sense that any little thing such as his height could frustrate him which he passes off as a joke on screen since it hurt what he holds dear, and stop him from filling this sort of empty void that’s been irking and limiting him as a person in many ways.
It also gives him confidence to be able to fully protect his loved one in Winry which to him, also helps her to have faith in his strength, encapsulating the themes; the importance of protecting what you love & beauty of humanity to overcome pain through perseverance and time.
Winry is Ed’s role model (similar to Trisha) so it’s only natural he would be mad if he can’t live up to her expectations or of the sorts. They’re human, of course they would have standards, naive to think otherwise. Teens obsess about their height or lack thereof all the time.
Ed’s a realistic depiction of male insecurities, desire for self-betterment & troubles in relationships between lovers.

His individual flaws are contributory to what makes his journey so endearing, compelling & earned. Winry is his emotional support and he wants to be hers.
One thing to mention is that the repetitive nature of said joke makes total sense. It happens too frequently that it annoys you? Good. Now you can feel the same frustration Ed has had to live with his whole life.
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