Similarly in the Darker and EdgierAdvance Wars: Days of Ruin, the defeated Admiral Greyfield tells Lin she'll be just as bad as him if she kills him, although in this case, he's just deliberately invoking the trope in a panicked and desperate (yet strangely Genre Savvy) attempt to save his own life. She admits that he's completely right, then shoots him anyway.
Similarly, Waylon does this to Will in their final battle. Will admits it, but informs Waylon that this doesn't give him the moral high ground.
In Mega Man Zero 4, Dr. Weil desperately bluffs Zero and tries to convince him that killing Weil would be stooping to his level of villainy. In an unorthodox move, Zero kills him anyway, making note at how he never considered himself a hero to begin with.
Though never conversed, a much sadder example involving White and Grey Morality exists with Zero and Harpuia, given how both are fighting for the same goal.
Done rather sadly in Mega Man 2: The Power Fighters, where Mega Man's solo ending had Dr. Wily pointing out Mega Man's senseless destruction of robots in the act of peace for humans and robots. This puts Mega Man in guilt long enough for Wily to escape by the time he is cheered up by his friends.
Inverted in Mega Man Star Force, with Mega Man Geo-Omega (the protagonist, and a good guy) telling Harp Note that he is just like her, in an effort to get her to join forces with him. Not only does it work, but it is actually true as both of them have previously lost a parent.
Metal Gear has Big Boss, an antagonist whose ideology of perpetual, honourable warfare lingers on through his unkillable son, Liquid Snake. It all seems the usual completely bonkers nonsense, until you're put into his shoes at the start of the third game and get to see what he went through before he formed the Foxhound unit and started trying to create a military nation to leave soldiers free to do battle. He suffers through the same betrayals and manipulation that the series protagonist, Solid Snake, has gone through, and at the end is just as alienated and bitter. It leaves a potent, unstated message about how someone's past experiences don't control their future.
A clearer example is towards the end of the first Metal Gear Solid. Liquid is talking about bringing about his father's vision of a return to warfare. When Snake claims that he doesn't want that kind of a world, Liquid's response is a CMOA.
Liquid: So why are you here, then? Why do you continue to follow your orders while you superiors betray you? Why did you come here? (Snake fails to answer.) Well... I'll tell you then. You enjoy all the killing, that's why.
Psycho Mantis does give a similar statement to Solid Snake. Well, sort of...
Psycho Mantis: I've seen true evil. You, Snake. You're just like the Boss... no, you're worse.
A more direct use of this was shortly after Psycho Mantis revealed what he did to the village:
Solid Snake: Are you saying you burned your village down to bury your past? Psycho Mantis: I see that you...have suffered the same trauma. (Mantis laughs feebly.) We are truly the same, you and I... The world is a more interesting place... with people like you in it. I never agreed with the Boss's revolution. His...dreams of world conquest do not interest me. I just wanted an excuse to kill as many people as I could.
In Assassins Creed I, mad executioner Majd Addin attempts to pull this on Altair, explaining that they aren't so different and that he would have done the same were he in Addin's position. Altair's response is to agree that indeed, he once may have, until he discovered what awaits such people - demonstrated by stabbing Addin in the neck.
In Assassins Creed II, the first mark (who got Ezio's father and brothers executed) makes the excuse, "You would have done the same...to save the ones you love." Ezio agrees... so he goes through with the killing.
In Oni, at the end of the Rooftops sequence's ninja bossfight, the main character exclaims that she has nothing in common with him - then breaks his neck with her boot.
Mukade: Does your blood burn when you kill? Mine does. Konoko: Stop it... Mukade: We writhe inside as we are torn apart to make way for what we will become. Surrender to it... Let the bliss of oblivion free you all your doubts and fears! Konoko: You're one of Muro's thugs, nothing more! Mukade:(laughs) We shall see... (Konoko beats the crap out of Mukade) Konoko:(thinking) Griffin encouraged me not to look too deeply into my past. Seems like there was a lot he didn't want me to know... I could feel the ninja and I know he could feel me. Why? What am I becoming? Are we the same...? No, I have nothing in common with him. (kills Mukade)(aloud)Nothing!
Panda King: Why should you care if I bury a few worthless villages in snow? You are a thief, just like me.
Sly: No that's only half true. I am a thief - from a long line of master thieves. While you... You're just a frustrated fireworks artist turned homicidal pyromaniac!
In the third game, Big Bad Dr. M uses this with Bentley because they were/are the smart guys of their group, with Dr. M stating that Sly's talks of Friendship is just an inherent Cooper lie. Near the end, Dr. M grudgingly admits that Sly's and Bentley's friendship might be real after all.
While it does depend on how you roleplay The Hero, your half-brother Sarevok in Baldur's Gate is implied to have several similarities to you. Perhaps the most damning evidence is a vision in Throne of Bhaal which shows that, had your positions been reversed, you each would have ended up exactly like the other. You can't fulfill this trope any more than that.
He has a mask which is never removed, he is shrouded in mystery, needs to sneak around lest he get shredded, and punishes enemies who let him get behind them. Now which Team Fortress 2 class are we talking about, the Spy or the Pyro with a Backburner?
The RED and BLU Teams are also Not So Different. To the point that they're both identical aside from their colors.
In The Suffering, Horace compares himself to the protagonist Torque in several scenes, though he often encourages him against becoming too much like him:
You had a wife, right? Didja love her? How far would you go to make sure she stayed yours? When you get mad, you feel you could kill a man, rip him apart with your bare hands. You ever feel that way? Maybe you're not like me, it's hard to say. Ya gotta fight it. Don't let this place do to you what it did to me.
In Grand Theft Auto IV, Niko is driven for revenge against the guy who sold out him and his friends for $1,000. When he finally confronts the guy, Darko Brevic, he is asked how much he charges to kill someone. It seems that Niko knows that Darko is right as it shows in his choices: if he pulls the trigger on the guy, he feels empty and unsettled; if he doesn't and lets Darko go, Niko still feels angry but also a little bit better at the same time, since Darko is in a very, very sorry state and will continue to live on in suffering.
Darko also resembles Niko very much physically. Pretty unsettling...
In Fallout 3, if you confront the murdering, inbred, cannibalistic residents of the town of Andale about their unsavory habits, their leader demands to know how many people you've killed. And throws 'judge not lest ye be judged' in your face, to boot.
In Legacy of Kain: Soul Reaver, the final battle includes Raziel confronting Kain about raising his vampire lieutenants from the corpses of prominent Sarafan (vampire hunters):
Raziel: The Sarafan were saviours, defending Nosgoth from the corruption that we represent! My eyes are open, Kain... I find no nobility in the unlife you rudely forced on my unwilling corpse! Kain: You may have uncovered your past, but you know nothing of it. You think the Sarafan were noble? Altruistic? (laughs) Oh, don't be simple. Their agenda was the same as ours!
This is shown to be true in the ending of Soul Reaver 2, when it proves that the Sarafan were controlled by Moebius, The Dragon of the series, and thus are bigoted and self-righteous. Raziel and his past, human self share this dialogue:
Human Raziel: You're a righteous fiend, aren't you?
Raziel: We both know what you truly are. You're no better than the vampires you so despise. A voracious parasite, masking its hunger within shrouds of righteousness!
In Warcraft 3, Mannoroth taunts Grom Hellscream, saying that they are the same. Grom responds by screaming defiance and charging forward to kill him.
In the World of Warcraft quest chain required to forge Shadowmourne, the Lich King includes this argument in his Break Them by Talking to you as you steal the souls of your fallen Scourge enemies. Darion Mograine, however, challenges you to kill without being consumed by its power.
In a Duskwood quest, when you learn that Stalvan Mistmantle killed his studentand her lover when his feelings for her were not reciprocated, his brother Tobias is horrified at this and confronts the now undead Stalvan, who confirms this. Stalvan then suggests that Tobias is feeling what he did- enough rage to kill someone- and Tobias transforms into a Worgen and fights him alongside the player. After Stalvan is defeated, Tobias has a My God, What Have I Done? moment, but when you turn in the quest, he's calmed down and has concluded that it's up to him whether he truly becomes a monster.
The Wolfheart novel has this in spades, particularly with respect to the contempt King Varian Wrynn of Stormwind has for the Worgen, specifically for Lord Genn Greymane. Slightly subverted in that Varian doesn't particularly have anything against the Worgen in general, but the only ones he know are those from Gilneas, who he feels abandoned The Alliance in its hour of need. Malfurion is the one who tries to persuade both kings (mostly Varian) that they are not so different: both care about their respective people, both want to help the Alliance. Of course, the biggest similarity turns out to be the fact that Varian is revealed to be carrying the spirit of the wolf demigod Goldrinn whom the Worgen revere. After both kings reconcile, Varian leads the Worgen in a charge that breaks The Horde's advance into Night Elf lands and sends the orcs running.
In Uncharted 2: Among Thieves, Lazaravic calls out Nathan Drake on all the mooks he's killed, saying that it makes Drake no different than he is. In context, the scene is a huge mashup of this trope, Moral Dissonance and Selective Condemnation.
In a non-villain example, in Deus Ex, Paul Denton mentions to the player the irony of how in order to defeat the one-worlders, the resistance forces, who support sovereignty and independence for the different peoples throughout the world, have to become a global organization.
It's never discussed, but in Human Revolution Jensen can slaughter his way through the TYM manufacturing and R&D facilities, re-enacting the brutal raid by TYM-associated augmented commandos on Sarif Industries from the prologue.
When Arakune and Hakumen meet in the Arcade mode of BlazBlue, the latter tells the former that they are quite similar down inside.
In Teach Me, Ms. Litchi!, Litchi notes that "[Kokonoe and Taokaka]'re more alike than they seem. There's only a thin line between genius and... Tao."
Shockingly (and many seem to forget), Kokonoe is dangerously Not So Different with Terumi, the very individual she hated herself. Both of them are not 100% human, and in the same time look down on them. They also placed themselves so highly in priority and damninsufferable in it, so the majority of Kokonoe's would-be Well-Intentioned Extremist acts end up failing because she's only thinking of her own desires, such as the nukes she stored, she doesn't care if she'll have to take the whole civilization and humans in it so long as Terumi is dead by her own hands, the humans can die for all she cares, the same thing as Terumi only thinks of how he can have his fun of making people around him suffer or hate him.
Lightning and Fang in Final Fantasy XIII have a 'not so different' moment, and the Datalog entry actually uses the phrase.
By the end of Mass Effect 2, Shepard and the Reapers are Not So Different. In the first game, Shepard and Sovereign are equally dismissive of the other. Shepard doesn't believe Sovereign is really "alive" — it's just a machine that can be broken. Sovereign considers organic life to be an insignificant aberration in the universe. When the second game begins, Shepard is revived and rebuilt with cybernetic implants to repair his/her skeleton, skin reconstruction, and synthetic fluids to restart his/her organs and blood flow. Then in the endgame it's revealed that Reapers are also cyborgs, in a way. New Reapers are created by pumping the liquefied organic material of millions into a mechanical Reaper superstructure. The new Reaper's form is based on the species used to create it. The partially grown Reaper encountered in the end is a Human Reaper, which makes it even more eerily similar to Shepard.
In the DLC, Lair of the Shadow Broker, the Spectre Tela Vasir, in her dying breath, will call Shepard out for condemning her for being a Shadow Broker hitman, when Shepard works for the terrorist organization Cerberus. She'll even point out that Cerberus did experiments on Sole Survivor Shepard's own squad.
Shepard and the Illusive Man are not so different; depending on certain decisions, Shepard is perfectly willing to let innocent people die to achieve his/her goals, and in The Arrival DLC the player has no choice but to sacrifice 300,000 innocent people to slow down the Reapers' invasion of the Milky Way. Couple this with the "Bring Down The Sky" DLC from the first game, where Balak asks "Who's the real terrorist here?" if you decide to capture him at the expense of the hostages he'd taken, and the conclusion of Arrival is a lot more depressing.
There's also Nassana Dantius, an amoral asari politician who's been targeted by Thane Krios for assassination. To secure her building, she hired dozens of Eclipse mercenaries and, when things got desperate, ordered the many salarian construction workers captured or killed, resulting in a massacre of unarmed workers who posed no threat. When Shepard finally makes it to Dantius' office, the asari bitterly claims that the Commander has killed countless people and is no better than her. A Paragon dialogue option from Shepard can refute this by telling Dantius that she kills people because she thinks they are beneath her, whereas Shepard kills people who give him/her no choice.
Saren and Shepard, though it doesn't become fully apparent until the end of the third game - and he died in the first. Saren advocated a partnership with the Reapers in order to spare organic life, and even becomes an organic/synthetic hybrid, with "the strengths of both, the weaknesses of neither," at the end of the first game. Shepard becomes one too when they are resurrected at the beginning of the second game, using similar tech. And then, at the end of the third, one ending resembles what he advocated - Synthesis, giving organics synthetic aspects and synthetics organic understanding, making all life into cyborgs of one degree or another. The strengths of both, the weaknesses of neither.
You'll get this at times in Iji if you kill too many enemies throughout the game. After all, Iji's trying to stop her species from being wiped out by unexpected alien threats. By the time Iji has a bodycount in the triple digits, those tasked with stopping her have exactly the same goal.
In Dirge of Cerberus when Vincent impales Azul the Cerulean on his own cannon by hurling it through his torso, Azul comments that Vincent, possessed by Chaos, is an even more of a beast than he is.
Big Bad Eve in Parasite Eve claims that Aya, the main character, is no different from her and that over time, her powers will help her evolve and grow stronger just like her. She also mixes this up with a few We Can Rule Together speeches, but Aya isn't buying any of it.
This is one of the main points in the plot of Tales of Symphonia. The hero of the game, Lloyd Irving, is outright compared to the Big Bad Mithos more than once. Mithos' final words drive the point home too. "Farewell, my shadow, you who stand at the end of the path I chose not to follow. I wanted my own world, so I don't regret my choice. I would make the same choice all over again. I will continue to choose this path!" It really makes you think on how close Lloyd would have come to being like Mithos if Colette had actually become Martel's vessel in the end.
Also in the same game, Zelos and Colette, while they're both considered protagonists, are often compared to each other due them both having status as Chosen, but are considered to be quite different from each other: Colette is a cheery if clumsy girl who always tries to help other people and look on the positive side of things, while Zelos is a loudmouthed, perverted cynic who isn't afraid to be blunt. However if you really look at their situations you see that they both try to hide their pains and insecurities beneath their smiles and pretend like nothing's wrong, which in both cases lead to negative consequences.
The main plot of NieR loves this trope too. Particularly when you find out that the Shadow Lord you've been hunting, the one who "kidnapped" Nier's daughter/sister (depending on the game version) Yonah, turns out to be the "real" Nier. The character you've been playing the whole game? Just a construct made to house the real Nier's soul. And both of them have the same goal - saving their daughter/sister Yonah from the one trying to take her away, no matter what.
In Radiant Historia, Stocke realizes that he likely would have turned out like Heiss if he had not found friends to give him hope in the future.
Malefor: Such determination to get here. It seems we share other qualities besides our color.
The Elder Scrolls V: Skyrim has a very subtle one when the player is talking to Paarthurnax, a dragon who has overcome his inherent nature to kill and conquer and destroy through thousands of years of meditation and self control. He points out that all dragons have an inherent desire to be essentially destructive bastards - and then comments that you, the player, being Dragonborn and thus possessing the soul of a dragon, likely have the same urges to kill and steal and destroy, just like all the dragons you've been killing along the way.
From the same game, there's also the songs "Age of Aggression" and "Age of Oppression", sung by bards in pro-Imperial or pro-Stormcloak holds, respectively. The song tunes are identical and both songs have parts where the lyrics are the same.
In Asura's Wrath, Augus claims this is true with him and Asura during the fight against him. Defied by Asura, they couldn't be more different since Asura is actually fighting for someone he loves rather than for its own sake and that is what gives him the strength to defeat Augus in the end.
In Star Wars Bounty Hunter, when Jango Fett and his arch-nemesis Montross face down for the final time, Montross says "We are the same, you and I." Fett replies, hilariously, "Now you're justbeing mean."
Big Bad Natla in the Anniversary edition of Tomb Raider pulls this trope on Lara Croft during the final boss fight. She tries to mess with Lara's mind saying how Lara is obsessive and selfish like she is and that trying to save the world is just an attempt to redeem herself and that in reality, her heart is as black as Natla's. Lara doesn't fall for it and proceeds to kick her ass.
During Nigel West Dickens's missions in Red Dead Redemption, John Marston frequently grouses about the Snake Oil Salesman and how he cheats people out of their money. Dickens never hesitates to point out that Marston robbed people of their money at gunpoint, and refuses to let Marston get away with his fumbling Robin Hood defense.
Pulled on Max Payne by himself in usual Self Deprecatiing style in the third game, where he considers how the Cracha Preto are gunmen on a payroll and wonders if that's all he is.
DMC Devil May Cry: Ultimately, both Mundus and Vergil see humans as subjects to be ruled. Dante even points this out: when Vergil expresses his desire to rule humanity, Dante responds "...you mean, like Mundus."
Sigma Star Saga uses a Meaningful Name to signify the similarity between your CO, Commander Tierney and the Krill leader, the Tyrannical Overlord. Both are willing to sacrifice their own homeworlds to get control of the bioweapon.
In Bio Shock Infinite, self-proclaimed prophet Zachary Comstock is considered not so different from Daisy Fitzroy or Booker DeWitt. All three of them are brutally dedicated to achieving their goals, whatever lies they have to tell or means they have to resort to. The reason for that is Comstock is an alternate-reality version of DeWitt that went through the baptism that DeWitt himself rejected.
In Warframe, this is one of the things Alad V says of you if you support the Corpus during the Gravidus Dilemma.
In Prototype, Alex Mercer displays intense distaste for Blackwatch and Gentek, especially the real Alex Mercer. He's ruthlessly violent and unfettered in trying to kill his way through them, not unlike Blackwatch's own willingness to stop at nothing. He also is determined to stop Elizabeth Green from triggering a Zombie Apocalypse. Come Prototype 2, and he fully intends to follow in her footsteps and even restarts the outbreak in Penn Station, like the original Mercer did.