What I believe is Steven's greatest flaw is his lack of selfishness. Now while that normally wouldn't be a bad thing, it's detrimental for a character like Steven.
I love Steven and many people have said that his kindness is his biggest weakness. But I believe it's his lack of selfishness.
I'm not giving him shit for being considerate and thinking of others. Hell, it's one the reasons I love him so much.
But I saw so many times in the show where I wanted him to be selfish. To put himself first. To just say: "Forget everyone else. I need to think of me." (The Heart Of The Crystal Gems Arc being a perfect example, especially since it was right after A Single Pale Rose)
Steven is one of those people that NEEDED to be selfish simply because of all the shit he was forced to deal with. And he no doubt thought it was wrong to be selfish.
But that's my only real issue with Steven. Other than that, I love him.