I know Nico's fatal flaw is canonically (is it canon?) grudges, but I feel as if it doesn't really match him all that much.
I would argue, his fatal flaw is longing, or a general want for more.
He always seems to be wanting something, to be searching for something or to get what he wants. He's always missing something.
Say, for example, in either tbotl or tlo he brought Percy to Hades in exchange for knowledge about who his mother was,
He was longing to know his family, to understand his past.
And after he lost Percys trust, he was longing to prove himself a good person, he helped save everyone during Manhattan and even though he wasn't explicitly looking for anything, I think he was just genuinely doing the right thing, I think he still wanted to prove he wasn't plotting against anyone.
His longing for family, or someone who doesn't distrust him, shows through his resurrection of hazel, and while yes, again, he was just genuinely doing a good thing, and he thought she deserved a second chance, he still wanted someone to like him. Someone to call a friend.
He seems to always be longing for the past back, to have Bianca and his mother again.
I don't have much evidence, but in my humble, non canon opinion, Nico di angelo yearns for so much more, all the time.