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Shinji is the epitome of all the hatred I have for most of the modern mech genre. Whiney teenage boy inherits incredibly powerful mech, but is too much of a bitch to pilot it. Most the anime revolves around them trying not to be a little sissy fag.
Why can't we have more Guy from GaoGaiGar? Why can't we have more Sanger from Super Robot Wars? Why can't we have more Simon from Tengen Toppa Gurren Lagann (except for that one part)? I watch mech anime to see big ass mechs fighting, not to see some faggot in high school bitch and moan for three episodes then fight for a few minutes. If I wanted to see story above all else, I'd watch a slice of life anime or something.
Imagine how shitty Berserk, Hokuto no Ken, Dragon Ball, Toriko and other popular anime/manga would be if the protagonist was as much of a loser as Shinji is.
Mech anime can get away with the protagonist being a twat because they're given the mech. It's used as a crutch to allow the characters to be overly emotional and weak, yet still strong enough to defeat adversaries. As long as they know how to pilot, it doesn't matter how pathetic they are as a human being.