One thing that annoys me with the Bob/Syndrome conflict is Syndrome`s motivation and how Bob was responsible for it
Regarding Syndrome/Buddy`s motivation to become a villain, the thing is that he`s given a relatable and understandable reason for doing what he did to Bob: Bob deliberately rejected Syndrome for selfish and egotistical reasons (for wanting to work solo), so it was easy to symphatize with Syndrome for it. So Bob was essentially responsible for what he did to Syndrome, as it was his choice of rejecting him.
Bob and Syndrome could`ve resolved their conflict and made peace, because Syndrome truly had vulnerable reasons for becoming evil. And Bob could`ve actually taken actual responsibility for what he did, as his apology to Syndrome wasn`t particularly sincere and was half-baked. So it was disappointing how the story essentially threw out the closure and just treated it one-dimensionally. As Syndrome was defeated, without having his redemption. And Bob just got away with what he did to Syndrome.