Lampshaded in the blog-novel Flyover City!, when the protagonist tells the big bad “…you know, we really aren't so different, you and I. Us, I mean.” - which compels the villain to list off all the ways they are emphatically not alike.
In the Whateley Universe story "It's Good to be the Don", Don Sebastiano gives this spiel to part of Team Kimba as he tries to lure them into his group. It nearly works.
In "Ayla and the Birthday Brawl", Phase successfully tries this routine on Jobe. But Phase is one of the main heroes, and Jobe is the son of a supervillain.
"You are wondering why I have given you this task. Why I trust you. My reasoning is not so difficult to understand, after all, we are similar. Your father is pushing you into a life you don't want, and my father... well... Let's just say I sympathize."
In Greek Ninja Sasha and Daichi are like this. After their fight, she tells him:
'You have no purpose. Life is mundane to you. Each day is just another day you have to get through with. You are surrounded by nothing that’s really important to you. So why should you fight to protect it? I understand cause that’s the way I was.'
Dragon Age: Redemption gives us the lead character Tallis and her first ally, Cairn, who serve two opposing masters. Over the story, it is revealed that the two of them actually have very similar moral theologies. Both of them have defied their superiors and went renegade to deliver their own brand of justice. Tallis killed an Orlesian when she discovered he raped slave girls, and Cairn attempted to kill the Saarebas when they slaughtered his family.
On several occasions, Taylor finds herself imitating the strategies of her antagonists, much to her discomfiture.
The supervillain Mannequin implies this while trying to recruit Armsmaster.
When Taylor is talking to Shadow Stalker in the immediate aftermath of Scion beginning his rampage, Shadow Stalker characterizes Taylor as being a copy of herself.
We're Alive: Riley's arc in Season 4 has her chasing down Scratch in a Roaring Rampage of Revenge after Scratch killed Angel. This parallels Scratch's own obsession for revenge against Pegs, who killed Scratch's brother, Latch. As Riley begins using more and more extreme tactics to try and catch Scratch, other begin to comment on the similarities between the two including Tardust and Scratch herself.