The weakness of Uchiha Sasuke was that after killing his brother, he had no goals, no reasons for living. Even more so because he had not thought of this yet.
The weakness of Inuzuka Kiba was that sometimes Akamaru was a much better partner than he himself was. But he was working and trying to change that, trying to become worthy of his companion.
The weakness of Rock Lee was his youthful determination, the same thing about him that Gai-sensei always praised. He didn't give up, no matter the odds, injuries, opponents, or potential risks.
The weakness of Nara Shikamaru was that he was lazy. Everyone knew that.
The weakness of Umino Iruka was that he cared. Cared so much for each and every one of his students and colleagues and it hurt him whenever something happened to any of them.
The weakness of Gekkou Hayate was a deep, hacking cough, one of the outward signs that his body was failing him, even if his mind refused to accept that.
The weakness of Shiranui Genma was that he always had to be on top of his game, something that is not humanly possible.
The weakness of Maito Gai was the he, like Iruka, cared. He cared too much about his students and teammates and he cared very loudly and outrageously.
The weakness of Hatake Kakashi was himself, his own mind. All the guilt and punishment he felt he deserved for the deaths of all of his precious people.
The weakness of Jiraiya was his appreciation of beauty, which often got him into trouble. Bone-breaking, cheek-slapping, raging female type trouble.
The weakness of Tsunade was blood. The blood of her brother and lover and everyone else she had failed, the blood that she could still see coating her hands.
The weakness of the genin was their inexperience. All the things they didn't know or hadn't seen or hadn't done. And being brand-new ninja, there were a LOT of things they didn't know.
The weakness of the chuunin was that they were in the middle. The knew a lot, enough to survive, but they still cared. Cared about all those around them and then every hurt those people got hurt the chuunin.
The weakness of the jounin was that they were the best. So much was expected of them and they were so well known that they had many enemies.
The weakness of the ANBU was that they didn't exist. The mental toll it takes when one isn't even sure one exists is just so great that few dared pay and those that did weren't willing to do so for very long.
The weaknesses of the Leaf ninja seem strange and very different, but they weren't. Because, really, a true Leaf ninja only had one weakness. So it was really easy for an enemy-nin to take advantage of it. But no one had ever taken advantage of this and survived. Because the one and only true weakness of the Leaf shinobi is always and forever...
Konoha.