Ryo tells Ango that the two of them are 'cut from the same cloth'. They're both stubborn, fast thinkers, are generally even the top of their classes and keep their cool in tough situations. Ango isn't happy to hear this, but eventually accepts it.
The two are also similar to their old sadistic teachers at the institution, especially Ryo. He begins to put Team Summer B through 'tests' that are similar to the potentially fatal situations they were put in prior to their Final Test, including leaving cards around the area before something happens. And when Koruri finds out how Ango has been treating Hana horribly including trying to rape her, which is a sore spot for Koruri, who had been sexually harassed by one of the teachers, she calls both of them out, stating that "that's what the teachers did!".
In Tsubasa Reservoir Chronicle, Big Bad Fei-Wang Reed explains "Syaoran" Li that the two have are wishing to obtain the same wish (reviving a dead person) the two have brought miseries to the people around them. In the story nobody ever denies this and the final chapters solidify this. However, it should be noted that "Syaoran" was just a puppet of Fei-Wang all along.
At least once Frieza tells Goku that they're alike, going so far as to point out that, as a Super Saiyan, Goku is as much a beast as he is.
Although neither knows it in the original Dragon Ball manga, the nameless Namek and Goku are very much alike. Both are aliens from worlds that were in distress, Goku's being outright destroyed. They both were raised in isolation away from the civilized world, lost their memories of their old homes, and had come to see the blue planet as their home. Their arrival on Earth also greatly impacted the planet, changing it forever. The difference between them is that the unnamed Namek, tainted by the violent nature of mankind, purified himself to become guardian of the Earth by splitting into two beings; Kami and Piccolo. In comparison, Goku lost his memories and was raised as a human by a kind old man, making him the most innocent and kindest of his species.
All of the villains from King Piccolo onwardshare many aspects with Goku. King Piccolo and his son Piccolo, as mention above, share similar backstories to Goku. The Saiyans all share Goku's love for fighting, pride in their power, and challenging themselves. Like Frieza, Goku has an enormous amount of raw natural talent, represents the strongest his race have to offer, and becomes just as sadistic as Frieza after turning Super Saiyan. After becoming perfect, Cell gains Goku's laid-back demeanor and gives his opponents sporting chances so he can enjoy the fight longer. Majin Buu shares Goku's love of food, fighting, playfulness, crude manners, and are much smarter than people give them credit for. With Beerus, they're both rather lazy outside of fighting, are food obsess, will seek any new challenge, and adore their friends more than their power. He is also among the most feared beings in the universe. The fact that Goku has a conscience and a set of morals are what set him apart from his enemies.
Some of the Z Team were shocked when they see 17 mercilessly kill Dr. Gero. Vegeta merely comments that it is no different as what Saiyans would do as he has no problem killing those he doesn't like.
Vegeta and Gohan are remarkably similar. Both lost their fathers at a young age and were kidnapped and raise by their fathers' mortal enemy to become weapons. While Gohan's kindness eventually makes Piccolo into a good person, Frieza nurtured Vegeta's dark nature and made him sadistic even by the standards of a normal Saiyan.
Baby, the first Arc Villain of Dragon Ball GT, constantly goes on about how the Saiyans are a bunch of violent, bloodthirsty barbarians, but his actions (enslaving an entire race, killing people without care) prove him to be just as violent and bloodthirsty.
Big Bad Alex Rosewater never gets sick of pointing out that hero Roger Smith is just as arrogant, power-hungry, and obsessive as he is, for manipulating a giant robot to fulfill his personal moral agenda.
Great Mazinger: He is a powerful warrior and accomplished swordsman, proud of their skills, that wants to protect his kind, and is capable of showing admiration towards someone who can match his skills, even if that person is an enemy. Both Tetsuya Tsurugi and Ankoku Daishogun fit in that description. Really, the bigger difference between them is Tetsuya is human.
Alviss and Rolan in MÄR. Both of them were orphans, victims of circumstances beyond their control. What differed was who took them in. Whereas Alviss was found by Dana/Boss, Rolan was found by Phantom, and their loyalties were based on those encounters. Alviss lampshades the trope in their battle in the finals, saying Rolan may have turned out more like him if it had not been Phantom who found him.
Mugen and Jin in Samurai Champloo. Pointed out by Fuu within her diary, much to both's displeasure. They're both morally ambiguous Blood Knights who differ only in personality. Although at first glance Jin appears to be the Standard Good Guy and Mugen appears to be the Token Evil Teammate, the series quickly establishes that Jin is also cold, irritable, and arrogant (esp. in regards to Mugen) despite his noble bearing and fine words, while by the second episode Mugen is already showing some heroic tendencies and concern for Fuu despite his claims of being a loner and hating everyone. Additionally, both Jin and Mugen enjoy the company of prostitutes, both Jin and Mugen love to fight and never back down from a challenge, both Jin and Mugen become better people as a result of Fuu's quest... the list goes on.
Yu-Gi-Oh! GX: Yubel informs Amon during their duel that he's just like her — they both destroy the ones they love.
Yu-Gi-Oh! has several, but a notable one is in the DOMA arc. Raphael, one of Dartz's henchmen, is convinced that even the nicest people have darkness in their heart, and tries to prove this to Yami Yugi by making him play the Seal Of Orichalcos field spell card that feeds off of the darkness in people. He succeeds, and wins as a result, in one of the most painful and depressing moments in the series.
In Tengen Toppa Gurren Lagann during Simon's final fight against Lordgenome, Lordgenome says, "There was once a man who fought as you do, unaware that his actions would lead to the universe's destruction." He's talking about himself, back in the day when he and the other thousands of spiral warriors unsuccessfully waged war against the attacking Anti-Spirals (which the Dai-Gurren Brigade battle in the second story arc, only to succeed), stating that Simon and he are not so different in that respect.
The Anti-Spiral himself is also an example. He swears that his people have no Spiral Energy and that he's opposed to Spiral Energy and anything it represents, yet during the final battle he suffers a Villainous Breakdown and ends up becoming Hot-Blooded himself.
Early on, when Kamina first met Leeron, he got creeped out and drew a blade on him. After making a Heel–Face Turn and being recruited into Team Dai-Gurren, Viral's reaction to Leeron was the exact same- although in the form of death threat from Gurren's cockpit.
Spike and Vicious have a moment like this during their standoff in the Cowboy Bebop episode, "Ballad of Fallen Angels":
Vicious: You should see yourself. Do you have any idea what you look like right at this moment, Spike?
Spike: (with a savage grin on his face) What?
Vicious: A ravenous beast. The same blood runs through both of us. The blood of a beast that wanders, hunting for the blood of others.
Spike: I've bled all that kind of blood away.
Vicious: Then why are you still alive?!
The anime also parodies this trope with Andy, Spike's one-shot foil whose similarities to the protagonist are so prominent as to be lampshaded repeatedly by the remaining cast. Naturally, the two hate each other's guts with a passion — well, Spike hates Andy's guts. Andy can't even remember Spike's name for most of the episode, which only serves to infuriate the protagonist further.
James and Jessie of Team Rocket on Pokémon would likely be two of Ash's best friends if they didn't spend all their time trying to steal Pikachu. They've proven time and again that, like him, they are compassionate and caring trainers who respect their Pokemon, and the rare times that they do something that doesn't involve underhanded methods, they can actually be rather competent trainers. If they tried to catch Pokemon the legitimate way rather than stealing them, they could probably be successful... Probably.
When Edward confronts Shou Tucker over his use of his wife and daughter as subjects in his experiments, Tucker says Edward is just like him, because Edward used alchemy to try to bring his mother back.
An older brother sacrifices his right arm, so that his younger brother can live. Now, are we talking about Edward Elric, or Scar's older brother? Ed forces Scar to have a flashback to his brother, who did a similar thing to protect Scar. Scar is also a lot older to emphasize the bond between brothers that they share.
In a conversation with Sgt. Fuery, Al comments that Ed dislikes Mustang because at heart, they are very similar when it comes to protecting their loved ones. If one takes a close look and compares them, they are indeed very similar to one another. Both are powerful Alchemists, both have seen the Gate of Truth, became State Alchemists at a very early age, are masters of a powerful and dangerous style of Alchemy, have made terrible mistakes they deeply regret, have a brother (in Mustang's case, brother figure) they love dearly, and both seem to have a thing for bossy, no-nonsense blonde women they have known since childhood.
Rare hero to villain instance: after Kimblee's chimera underlings are defeated and tied up, Alphonse asks them if they really have no family or anyone who cares about them. They respond that, being half-human monster-things, they can't exactly go home again. Al takes off his head to show them he isn't a normal human either, and if he can hope to get his body back, so can they, talking them into a Heel–Face Turn.
Edward had a similar moment with the Slicer Brothers after beating them in the 5th Laboratory, refusing to kill them despite being Animated Armor just like Al—precisely because they were Animated Armorjust like Al. Unfortunately, they got speared by Lust right before their ensuing Heel–Face Turn could have any effect.
Greed gives one of these speeches to Ed not too long before the final battle, explaining how even though what Ed is wanting to do is seen as noble and Greed's goals are seen as selfish, both of them are at the end of the day motivated by desire, and that "greed" doesn't necessarily have to be evil. Also, when Greed first fought Ed, Greed taunted Ed for being the kind of person who doesn't mind getting beat up but flips out when people he cares about get hurt, and ironically Greed turns out to be exactly the same in that respect.
May Chang comes from Xing's smallest and weakest clan, and her pet panda was also abandoned by its family for being small and weak. When hearing this, Scar decides to help find Shao May. Yoki explains this change of heart to May by drawing paralells to the Ishvalan Extermination where Scar's people were wiped out.
One of the big revelations is that humans share much of their DNA with their enemies, the Angels. Misato remarks on the tragic irony behind the fact that each race wants to exterminate the other despite being so similar on a genetic level.
A more personal reveal was the fact that Shinji and Gendo both suffered the crippling fear of hurting those they were close to, and being hurt in turn. Gendo's decision to send Shinji away was driven by this fear after he concluded they would both be better off if he did nothing at all.
Shinji also realises during the beginning of instrumentality that he and Asuka are very much alike:
Asuka: Even just the sight of you gets on my nerves! Shinji: Because I'm just like you?
Death Note: Both Light and L fall under this trope, engaging in roughly the same questionable activities in their cat-and-mouse game. For example, they both use criminals to test the power of the Death Note at least once during the story.
Lampshaded several times in the story, especially with L's true name: Lawliet, which is pronounced in Japanese like "low light."
Matsuda and Light are also Not So Different, as Matsuda admits to having occasionally thought that the world would be a better place if some people weren't in it. Later on, he starts to become seriously worried by how much he sees the world as having improved with Kira around, leading to something of a Get A Hold Of Yourself Man (minus the hitting) moment on the part of the other policemen. Then you have Mello, another detective investigating Kira, whose actions in pursuit of Light are so dreadful that it's hard to say that he's any better than his foe. Really. He's a lot worse. So much that the police is willing to accept Kira's help to take him down.
Near, who, before officially taking on L's name, is shown to be just as questionable in his methods as his deceased predecessor, if not more so. It's hard to go into detail, but a hotly debated issue is the accuracy of Matsuda's theory that he controlled Mikami with the Death Note. Not helped at all by Word of God, which states that Near is "dishonest" and "the more evil" of him and Mello. But many have found him to be simply maligned by L-Fangirls who see him as a Replacement Scrappy
Monster: Dr. Gillen invokes this towards the incarcerated serial killers he interviews. Since his sins actually appear to amount to being an emotionally distant husband, and getting competitive as a student to the point of cheating on ONE test, this seems a bit of a stretch.
Negi and Fate Averruncus are also not so different from one another. That's why they joined forces to save the Magical World.
The final battle of Zeta Gundam has a couple of speeches along these lines. Played straight in the case of Kamille and Jerid, and played rather strangely in the case of Reccoa and Emma. Also, there is a really nice scene in a theater...
In the anime version of PrétearFenrir even says at one point that Himeno is going to repeat her fate — to which Himeno immediately objects. Not only Fenrir actually got her powers from being in the same position as Himeno, she turned evil because of her unrequited love for the same person Himeno is in love with.
Astro Boy gets to hear one of these speeches every time he tangles with Atlas or Blue Knight. In fact, in Blue Knight's case it actually worked for a while.
Late in Code Geass, Jeremiah Gottwald asks Sayoko Shinozaki if it's chivalry (the same code of loyalty that he's tried to live his life by) that makes her remain loyal to Lelouch, despite being Japanese herself, and she agrees that this is probably the reason. Considering they spent the vast majority of the series on opposing sides, and tried to kill each other the first time they crossed paths, it counts. Both are much beloved Ensemble Darkhorses so the idea of them being a pairing soon entered fanon via Memetic Mutation based ENTIRELY on this small speech.
Much more important is the ending: When Lelouch and Nunnally confront one another, Nunnally reveals that she accepted control of the Damocles in order to focus all the world's hatred on the WMD-flinging space fortress, so that people could finally unite and move towards peace. As we learn at the final episode's climax, Lelouch had the exact same plan - except that he made himself the object of hatred, and then allowed himself to be killed so humanity as a whole could move on.
As foils of one another, it's obvious to the audience that Lelouch and Suzaku are Not So Different, and there are a number of instances when they realize this in the show. One obvious example in R2 being during the meeting at the Kururugi shrine, when Suzaku sees through Lelouch's lies because he recognizes that, like him, Lelouch is pained by having to cover things up in order to make the world better. Because of Schniezel's interruption, it's still a few more episodes before they actually manage to reconcile.
As the series goes on, Tsubaki is envious towards Kaori because she can communicate so well with Kousei due to her vast knowledge of music. It turns out that Kaori is also envious of Tsubaki because she knows everything about Kousei's life due to their shared childhood.
Nagi realized that Kousei and herself are this; both are always gazing, pursuing, and loving someone they can never have no matter how hard they tried. In Nagi's case, its her own brother; in Kousei's case, its a girl who like his best friend. She also realized that Kousei also afraid because of the sheer pressure before giving their duet performance in episode 18.
Naruto and Gaara. Their arc (and their eventual friendship) actually bases on them being Not So Different. This also happens in way too many fillers in the anime, particularly in the Temple of Fire filler with Sora. Not only did they initially start out as outcasts in their respective communities, but Sora even has part of the Nine-Tailed Fox's chakra within him. Also, in the Ultimate Ninja game, if you select Hinata's history mode, when you face Sakura she'll say that Hinata reminds her of how she used to be shy before meeting Ino, fighting you/Hinata for a good challenge, and offer encouragement and comfort if you/Hinata lose.
Pain also pulls this off in his fight with Naruto, pointing out that they both act out of their sense of justice and that they both desire peace, even if their methods are different.
In chapter 485, Naruto admits that he isn't too different from Sasuke, since he once harbored thoughts of revenge against the Leaf Village for his shabby treatment. He claims that if things had been a little different, their positions could have been switched.
In chapter 581 Kabuto says he and Sasuke are not so different because they both wish for the destruction of the Leaf Village. In response, Sasuke says "I'm not like you".
Don't forget Gaara telling Sasuke this as their eyes really matched their purpose of life: revenge.
In an interesting twist, one of Tobi's goals apparently is to make Naruto more like him. And given that he's actually Obito Uchiha, the good-natured knucklehead of Kakashi's genin team before he suffered a Freak Out, this is probably a case of I Hate Past Me. Naruto acknowledges this and says that, had things been different for the former, he might have actually admired Obito.
In A's, during Zafira's third fight with Arf in Episode 7, he says that he will serve his mistress regardless of whether what he's doing is right. He then says "You're the same type of beast as me... can you say you're any different?" While he is a guardian beast and Arf is a familiar (which Arf herself says is a difference only in terminology), he has a point considering that Arf had helped Fate gather the Jewel Seeds in the first season. Arf is left unable to articulate a response.
A variation: Habashira Rui and Hiruma have a moment in Eyeshield 21 where Habashira asks why their paths are so different when their methods are the same.
In One Piece, done inadvertently by Sanji when fighting Absalom: Not only they have a similar reaction to seeing a sleeping Nami in a wedding dress, but Sanji reveals that given invisibility powers, he would do little better than Absalom himself.
It becomes a bit unnerving just how similar Luffy and Blackbeard were when they first met.
It's been stated that both Crocodile and Gecko Moria were very much like Luffy in their younger days. In this case, they seem to serve as reminders of what Luffy himself may become if, as Crocodile did, he allows the harshness of the world to make him abandon his dream, or, as Gecko Moria did, he fails to protect his True Companions.
Then there is Hordy and his pirates who hate humans because they kidnap fishmen to be slaves. When they get power they kidnap humans to be slaves. One of the pirates is even making humans carry him similar to a World Noble.
As later revealed, Donflamingo and his younger brother, Rocinante, the second Corazon. While the brothers are starkly different with Donflamingo being a psychotic mad man and Rocinante being an honorable undercover Marine, both have short tempers when it comes to those they care about. Mess with Baby 5, a girl who cannot decline a question (like marriage) and is like a younger sister to Dofy? He'll wipe out the whole town. Refuse to treat a sick boy and in fact panic with unprofessional inaccuracy and disgrace? Rocinante will destroy the hospital.
Going all the way back to Drum Island, Sanji actually invokes the trope in a positive way. He and Luffy had earlier called Chopper a monster because he was a reindeer who could transform into a humanoid form because of his Devil Fruit. Chopper then sees Luffy's own Devil Fruit powers and asks Sanji about it. As a way to make up for the bad first impression, he goes on to say Luffy is "a monster," subtly pointing out that Chopper may be odd, but then so is Luffy.
Done with a positive intonation in Gaiking: Legend of Daiku Maryu. When Lee actually meets a momentarily-blinded Vestanuu, she lets him know she fights simply because she and the others of Darius believe that humanity attacked first and they're justified in defending themselves.
In YuYu Hakusho, Yusuke notices that he's some similarities with his opponent Jin, particularly enjoying fighting and a similar fighting style, and his acknowledging their similarities is slightly played up in the anime. After dying at Yusuke's hands, Toguro tells Genkai that Yusuke has the potential to become great, but might end up like him if Genkai doesn't make the right decisions.
Happened with Hiei and Mukuro as well, with Mukuro recruiting Hiei for the sole reason they they both grew up with terrible lives, and living in Makai, where it's a constant struggle for survival, that's saying something. Eventually (once Mukuro's revealed to be a woman) blooms into something of a tempestuous romance.
This is actually a major underlying theme in the story. Mainly in that demons are also Not So Different to humans. Demons are a designated evil and have no obligations to being good. Thus often making themselves out to be more evil. Well, at least in this show. But the series then introduces many humans who are just as evil if not worse than demons and many demons who have proven to be truly good-hearted like Yukina. In the end chapters of the manga, for example, announcer girls Juri and Koto, known for not being afraid to commentate on carnage during the tournaments, find a natural affinity for television. It's a sign that more-disciplined demons who learn to play by the rules (the most basic rule: don't exploit humans) can be accepted by humans as being rather decent folk.
In SD Gundam Force, Sazabi tries this on Captain near the end of their fight, in an attempt to lure him to the dark side. Captain's response?
Baccano! goes for a not quite good, but not quite bad thing in "Drugs and Dominoes", when Eve Genoard finally encounters Luck Gandor, the man who "killed" her brother after he killed three of Luck's friends, entirely unprovoked. Not only does she learn that he's not the monster she thought he would be but also that, given similar circumstances (namely, learning that Gustavo killed her father and other brother for his own personal gain), she would do the same without a second thought — the only reason she didn't blow Gustavo's head off then and there was because of Luck's intervention.
In 1711, while agonizing at the possibility of having to kill the envious fellow alchemist Szilard to protect some dangerous knowledge, Maiza asks "Are he and I really so different?" (As it turned out, they were different enough that Szilard completely lost his marbles and started killing people for the knowledge even while Maiza was still thinking it over.)
In Full Metal Panic!, Sousuke is subject to this kind of Break Them by Talking from Gauron in "The Second Raid". Gauron gets pissed off that Sousuke has been trying to fit in with normal people and have friends, saying that it's making him "weaker", and that it's a hopeless goal to have. He proceeds to go on about how they were a match made in heaven, and that Sousuke shouldn't deny it. It eventually ends with Sousuke shooting Gauron. Which was exactly what he was hoping for.
In the manga, Leonard Testarossa asks Chidori why she is more afraid of him than Sousuke, saying that Sousuke has killed just as many, if not more people than Leonard.
Similarly, as much as Jariten berates Ataru for his perversity and gets angry when Ataru hints at Ten's own lustful thoughts, he's really no better than Ataru, as he's well aware that being a cute little baby makes him much more attractive to the girls then Ataru.
The same with Mendou. He acts like he's the opposite to Ataru - respectful and chivalrous to the girls. However, he's really just as much of a pervert and prides himself on using his money, status, and good-looks to lead girls on. Lum, herself, even points this out and doesn't like Mendou because of how fake he is. And later, Shinobu realizes this and leaves Mendou behind.
Alucard also notes how similar he and the Major are, as they are both lovers of war who destroy their enemies and allies alike in pursuit of their mad ambitions. The big difference between them turns out to be that, when offered immortality on the verge of death, Alucard accepted while the Major adamantly refused.
It turns out that the two who were really Not So Different all along were, in fact, Alucard and Anderson, to the point that it actually brings Alucard to bloody tears. Though the two originally had a Red Oni, Blue Oni thing going on, Alucard appreciated him as his dearest enemy and tells him that if Anderson killed him, he would be honored. That doesn't stop him from going full force against Anderson to test him, though...which ends up backfiring hard when Anderson uses a Deadly Upgrade and essentially becomes a tool of God in order to finally kill Alucard. Alucard, who sold his soul to the devil in order to live as a vampire, cries and gets extremely pissed because he didn't want Anderson to become a monster like him. After all, a monster of God is still a monster. But Anderson doesn't care because he's always seen himself as an instrument of God, so he sees the other side of the coin: a monster of God still serves God.
Afro and Justice from Afro Samurai becomes a clear case of this over the course of the series. Justice is the reigning Big Bad, having killed Afro's father before his eyes when he was young boy. From that day on Afro led his life on the path of vengeance to kill Justice. While his reasonings for wanting to kill Justice is sound, Afro uses rather extreme measures to achieve his goals essentially making him a Villain Protagonist. By the end of it, the viewer comes to realize the only thing that really sets Afro apart from the Big Bad Justice is that Afro is simply the viewpoint character. It was even stated by Word of God that Justice had his own legitimate reasons for killing Afro's Father, making Justice a Designated Villain more than anything else.
Gunslinger Girl: Triela comes to think this of Distaff Counterpart Pinocchio (the young assassin she'd dedicated herself to killing) at the end of Il Teatrino. Flashbacks reveal that their backstories are remarkably similar — both are victims of child abuse rescued by their surrogate fathers, and who judge their own worth solely by their ability to kill for that 'father'.
In Slayers, it is revealed that the only differences between Gods/Shinzoku and Demons/Mazoku is the type of emotions that feeds them and the magic that can be called upon from them (Shinzoku being HolyMagic and Mazoku being Black Magic.)
In Bakuman。, Nanamine, having revealed his truecolors, tells the main characters, whom he's a fan of, that they should understand his lack of trust in editors and plan to get ahead by releasing his rejected one-shot online and consulting 50 people for advice by saying that they had to defy their editors and make waves in the past, and that "Tanto," a work that they were dissatisfied with enough to want to end, is the result of them listening to their editor.
In the Berserk manga, Puck chastises Guts - who at the time is just as vicious as the monsters he hunts for - for being so cruel to Vargas, a kind but revenge-driven man who wants the apostle who mutilated Vargas and forced him to watch as he ate his wife and children dead, saying that they weren't much different and should consider each other allies. Guts laughs it off, but later reconciles to himself that he and Vargas weren't so different after all, since he and Guts shared the same cruel fate when encountering apostles.
Another, very disturbing one is the result of Fridge Horror. Look what Femto did to Caska and Guts during the Eclipse, now look back at volume 3, where Guts is forcing young Theresia to watch as he brutally tortures her father (The aforementioned Count, who himself is quite the Tragic Villain) right in front of her. It causes me to shiver everytime I remember, because you can just see how close Guts is to turn into what Griffith had become!
At one point during the Golden Age Arc, Casca even pointed out that Guts wasn't so different from Griffith when their personal ambitions and dreams were involved. She basically called them both out as self-centered bastards who didn't give a damn about her feelings or well-being in the end so long as they got what they wanted (which also has a lot offridge implications as the story progresses - literally).
Also appears in the non-canonical video game Sword of the Berserk: Guts' Rage, when it is revealed that both Guts and Balzac, the game's antagonist, had not-so-different tragic love stories.
Once the enmity ends between Ichigo and Uryuu, it becomes very clear, very quickly that the two are not so different. Neither of them are willing to accept such a claim but, while the pair may look dissimilar on the surface, everyone in-universe who knows them can see just how alike they really are. It's a source of great amusement for their friends, in fact.
Subverted between Kyouraku and Starrk. Assuming this is part of why Starrk loses, as he starts to assume too much about Kyoraku's methods until Kyouraku reveals that he may share Starrk's Brilliant, but Lazy tendency, but the truth is that he's a Confusion Fu personality which Starrk dislikes.
A major one for the Thousand Year Blood War Arc. Vandenreich leader Yhwach reveals that Yamamoto was once every bit as brutal as him, something both are aware of but hold in different perspectives.
Heaven Canceller in A Certain Magical Index points out to Accelerator that he and Touma are not all that different in their determination to protect those they care about.
A few characters lampshade how both sides of Science Vs Magic have similar methods and goals. For example, Academy City's goal of creating a Level 6 Esper through science is similar to the teachings of Gnosticism.
Touma and Othinus come to this conclusion about each other after their conflict in New Testament 9. Othinus trapped Touma in a series of horrible alternate worlds in an effort to break his will, but it helped him realize that she had also been cast out of her original world and had been trying to get back. She considers him the only person who understands her.
Leiji Matsumoto really loves this trope, but it's more obvious in Galaxy Express 999 (in fact, the series revolves around the concept that the only difference between humans and mechanized people is that the mechanized people feels less limited by their robotic bodies).
Played horribly straight in Space Battleship Yamato. For most of the first season we are repeated that the Gamilas are evil for what they've done to Earth and Mankind, but when the Yamato is about to reach Iskandar we find out that the Gamilas did what they did because they had no other choice but to adapt Earth to them if they were to survive, and that included the extinction of Earth's original life forms. Kodai has to acknowledge the Not So Different angle after the battle to reach Iskandar has devastated Gamilas and destroyed its cities, killing billions, by the very actions of the Yamato crew.
The leader of Gamilas, Dessler, also falls into this trope in the series followup, the TV series 2. After being The Dragon for the Comet Empire, Dessler realizes after the end of combat with Yamato that Kodai cares as much for Earth as Dessler did for Gamilas. Thus began the Heel–Face Turn...
Nadia: The Secret of Blue Water: When Jean and Hanson stop fighting over the blue water, they realize they're both mecha geeks and simultaneously squee over the Nautilus. For the last seven episodes, these two have been antagonistic but thanks to Enemy Mine they become good friends.
A variant occurs in Mobile Suit Gundam SEED when Uzumi Nara Atha, leader of the neutral nation of Orb, notes that the warring factions of ZAFT and the Earth Forces, are not so different; both are genocidal regimes who are unwilling to compromise or seek a mediated solution. He draws particular paralells between their leaders, the Natural-hatingPatrick Zala and Coordinator-bashing Muruta Azrael. Both men would go ballistic if they heard this.
In Mai-HiME, Natsuki realizes that she is Not So Different from her bitter enemy Nao when Nao reveals that her father was killed and her mother was rendered comatose in a robbery, leading her to trick men into soliciting her for Enjo Kosai and robbing them in revenge and for her to distrust anyone other than herself. Natsuki lost her mother at a young age and her father abandoned her, leading her to be similarly vengeful, as well as distrustful of others until she met Shizuru. As a result of this, Natsuki prevents Shizuru from finishing off Nao after destroying her Child, in spite of everything Nao did to her.
InuYasha: Inuyasha and Sesshoumaru turn out to be this. They even follow the same Character Development path (although it takes Sesshoumaru longer and the anvils dropped on his head need to be more vicious to get him to pay attention). This is lampshaded a couple of times in the manga, usually Played for Laughs, such as when Toutousai deliberately provokes the pair into trying to kill each other then complains that their identical short tempers prove they're brothers.
Tomoe and Nanami, the two main characters from Kamisama Kiss come from radically different backgrounds (Tomoe is a Little Bit BeastlyKitsune familiar to a Shinto God and Nanami is an Ordinary High-School Student) and have very different personalities (Tomoe is a Jerk Ass while Nanami is a Type B Tsun Dere). However, as the story progresses we eventually see they have more than a few things in common. Namely both have pretty bad tempers, both speak their mind no matter what the situation calls for, both have a rebellious streak in them and don't behave like society expects them to. They also have had similar experiences in life: both have lost a loved one that they deeply cared about, both were abandoned by someone they trusted and they are both disliked in their own worlds and in the divine world.
Hiyori: You were right. We are the same. We don't want...
Ikaros: ... the boy we love to die.
Bokura no Kiseki: After Yanuma loses it and attacks Meguro in a desperate bid to get people to respect him, the main character Harusumi has a moment of this. He says that Yanuma's desire to force everyone to respect him with his rank in the past and his superior magic is similar to the desire Harusumi had back in the prologue to attack the people who were bullying him with dangerous magic.
Nena Trinity and Louise Halevy in Mobile Suit Gundam 00 qualify. In the first season, Nena shoots at Louise's family in frustration over having to work while others have fun, crippling her and killing the rest of her family. In the second season, Louise lets her hatred and desire for revenge rule over all her actions as she oversees the massacres of thousands. Eventually, the two meet after Louise's Super Prototype Regnant ambushes Nena's outdated Throne Drei. Hearing Louise's desire for revenge, Nena counters by saying she is doing the exact same thing, since she lost her brothers soon after the wedding massacre (and had to live an even worse life than Louise). Unfortunately for Nena, because she was the one who killed Louise's family, Louise shrugs off her comments and plea for life by citing that she will never forgive her... and kills her brutally. The end result shows Louise now as disturbed and psychopathic as Nena, and Louise pays dearly for it in the movie.
In The Familiar of Zero, humans and elves had Fantastic Racism toward each other. Several characters learn that other than cosmetic differences, humans and elves behave almost the exact same way in similar situations. Arie, an elf with a great hatred for humans, eventually befriends Guiche when he sees that Guiche's interactions with his girlfriend Montmorency mirror his own interactions with his girlfriend Luctiana.
In Puella Magi Madoka Magica, the respective sacrificesMadoka and Homura have made are motivated by exactly the same goals: to protect the people they love and find a purpose in life. And when they become Witches, both decide to use the same method: forcibly trapping their loved ones in a Lotus-Eater Machine. These similarities are the biggest reasons why Homura is not seen as completely villainous.
In Episode 3 of Attack on Titan, Eren is having a lot of trouble mastering the basics of the Maneuvering Gear. He asks various characters for help, but none seem to want to help him at first. Reiner and Bertolt, on the other hand, ask him why he's so determined to be a soldier, then tell him that they were also from a Doomed Hometown. They go with him to help him a bit with some extra training at night in an attempt to help him pass the training. This comparison becomes a bit more...interesting...when it's revealed that Reiner and Bertolt are also Not So Different from Eren in that they're both Titan Shifters.
Parodied in Ouran High School Host Club between the titular club and the Zuka club. Both are hammy, often cosplay, wear lavish costumes, have legions of fangirls and want Haruhi to stay/join them.
Tamaki and Haruhi. Both have an uncanny ability to see through a person's core problems and (eventually) knows what to say to make said person feel better or understand what they need to do. They have a Missing Mom (one deceased, one missing) and they are the only members in the club who don't have siblings.
Akihito and Mirai in Beyond the Boundary. Mirai early attempts to distance herself from Akihito because she believed she is alone, cursed and has no one to rely on, unlike him. In episode 4, he tells her she is being foolish. When she sees his Superpowered Evil Side awaken and his "friends" aggressively attempt to control him, she realizes how wrong she was about him.