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Yosuke from Persona 4. (Posted this in reply, got removed for "natter", so putting it here for discussion.)
Yosuke likely doesn't apply here. The "Jerkass" part is missing. He might not be the most sociable, but he at least tries to be pleasant and friendly. The only reason people dislike him is because he's the son of the owner of the big-bad store chain, not because he himself is an unlikable character. He actually goes out of his way on several occasions to try and make things go as smoothly as possible for everyone working at the store, even if he does snap on one occasion due to being way too stressed out (mostly because it's not even his job to manage schedules and such, he just helps out because everyone around there knows him anyway).
Yeah, he's a bit of a jerk, but definitely not to jerkass levels. I'd definitely say it's misuse.
The Woobie part is based on opinion, but the jerkass part shouldn't be. And I just don't think he fits.
And now Yukari from Persona 3 is on the list as well. As the entry says, she can "be a bit surly on a bad day", but that's the same for everyone. Occasional negativity and snark does not make someone a jerkass. To be a jerkass, they have to have that attitude continuously. IF ANYONE from the series fits here, it would be Shinjiro from P3.
I'll be removing both Persona entries, and pointing the discussion here if someone has something to add.
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How well does it match the trope?