Changed the mecha from an unfeeling mechanoid with unlimited energy that is easily repaired to a biological entity that bleeds, feels pain, needs an extension cord for power, and may even have a personality.
Most super robot shows have a teenage mecha pilot and a long-absent father who designed the mecha. So Evangelion shows how traumatizing it would be for a real teen to fight in a giant robot — and what kind of father would abandon his son to design the robot.
Half the cast is made up of what seem at first to be stereotypical anime characters. As the series progresses, however, they are revealed to be severely messed-up people with the same sort of problems that would be expected of real-life tsunderes, hard drinking party girls, and lovable sex maniacs.
Quite a few old super robot shows featured mysterious, alien villains with very lightly defined motivations; cue the relentless attacks of the Angels, alien (or not) assailants on whose motives, constituents or psychology we have a little idea of, simply malevolent MacGuffins to enable the story to play with 'giant robot' tropes. They also happen to get progressively creepier, and more unexplainably eldritch as the show progresses. Most importantly, there is an emphasis on showing the fear and uncertainty that comes with fighting an enemy that is just plain undefinable, thus showing how it just takes a little to turn an idealistic, formulaic Super Robot anime into a depressing Cosmic Horror Story. Various factions within the series vie for the opportunity to take down the Angels in the way they deem most appropriate, with the winner, of course, being the one that causes the most collateral damage.
Tokyo 3 is all but destroyed by the end of the series, and its populace is either dead or evacuated — a sharp contrast to the likes of most examples of the City of Adventure.
In some ways, Eva resembles the early days of the Real Robot Genre. Shinji Ikari has quite a few similarities with Amuro Ray, the most iconic mecha protagonist in anime history. While Amuro's relationship with his father is not nearly as bad as Shinji's, Amuro's father does go insane while building the RX-78 and due to his injuries in the first episode (which Amuro himself caused). Amuro is just as "whiny" as Shinji, but is forced to accept responsibilities in the military hierarchy and grows to maturity through that. Even his reaction to his accidental killing of Lalah resembles Shinji's after killing Kaworu.
Later arcs notwithstanding, Rurouni Kenshin can be seen as a deconstruction of the Jidai Geki genre. Being a samurai isn't just a thing of honor and swordfighting for either your master, your beliefs, or other causes, and it leaves huge mental and social scars on those who survive it. And then, all of a sudden, everything that made being a samurai "cool" disappears because society isn't feudal any more, owning a sword is illegal, and even if you could get your hands on one your enemy might decide to use guns instead...
The original Gundam series (parent of the Real Robot Genre) could count as a deconstruction of the Super Robot Genre too. To even begin to be able to pilot the Gundam, Amuro already had a strong background with electronics, and the Gundam's manual. His early fighting is clumsy and ends up blowing a hole in his home space colony that kills unknown numbers of civilians and leads to his father suffering brain damage that drives him to insanity. His early battles shook him greatly, and Char kicked his ass easily in their early fights, despite being in the less advanced Zaku 2. Amuro is also a whiny brat of a kid and is forced (through good use of the Bright Slap and a stay in the brig) to accept his responsibilities. Of course, in later Real Robot shows, the flavor of the Super Robot Genre would kick in...
And that Super Robot Genre flavor that kicked in the later episodes of the show is itself a bitter deconstruction of the "loser mechs", as Gundam Sousei would point out.
Now and Then, Here and There deconstructs the old anime stock plot of Trapped in Another World. It starts the typical basic premise of "Ordinary High-School Student meets Mysterious Waif and gets whisked off to a world locked in a great crisis." it got worse from there. And then shows how relevant an Ordinary High-School Student would be in such a situation (not at all), how traumatizing it would be for someone from a peaceful society like late twentieth/early twenty first century Japan to be suddenly trapped in the middle of a war zone (extremely) and how likely it would be for anyone from that world including the waif that brought him there in the first place to even lift a finger for a naive and clueless outsider, much less form True Companions or a harem around him (not very).
Actually, it's more than that. The series includes other characters who are or have been in similar situations, like another king (Shoryuu), two kirins or "sacred beasts" (Enki and Taiki), a peasant girl (Suzu) and, in the anime, two of Youko's classmates (Asano and Yuuka). All of them have huge problems with the premise and have to deal in different ways.
Premise: being kidnapped to a strange magical world as the chosen one is wonderful! Decon: no it's not. But per the above comment, that deconstruction isn't allowed to stand as a universal statement. Youko represents the normal reaction, especially when the benevolent kidnapper is himself waylaid and Youko herself subjected to abnormal stress. Yuuka is the one who wants to live the Changeling Fantasy and might have adapted well save for not being the chosen one at all. Suzu and Asano don't even get the illusion of being chosen, and deal poorly, though Suzu's pretty lucky. OTOH, Shouryuu and the two kirin really are Chosen Changelings, don't get waylaid on their way back, and do as well as the original trope would have it. (Taiki's later tragedy is independent.)
Premise: a bunch of arbitrary rules and gods. Decon: a bunch of the main characters eventually wonder about the rules, doubt the gods, and try to ask the gods for rules clarifications. Storming the Heavens isn't a practical option, so they don't.
Premise: fantasy monarchy is wonderful! Decon: except when it isn't. A filtering system gets rid of the worst cases, leaving the best ones as immortal enlightened despots, avoiding the succession problem. A kirin with contact with modern Japan snarks about possible democratic alternatives anyway.
Premise: polite strangers help the bewildered, inexperienced main character/s out at critical moments in their adventure. Decon: if it serves the strangers' interests, especially regarding material gain. When it doesn't, the main character eventually has to actively choose to not let the subsequent behavior of most peasants turn her to The Dark Side.
The visual novel School Days (and its anime adaptation) is a Deconstruction of the harem genre and the Slice of Life romance genre. The lead, after finally dating the sweet girl he's been lusting after for ages, finds that dating her feels more like work and less fun, so he pursues and has sex with one of the other girls who wanted him. Shortly after, he decides to sleep around, with no regard for the consequences and no desire to devote to a serious relationship. When the girl he first began cheating with discovers she's almost sure to be pregnant and confronts him, he wants nothing more to do with her, and after everyone finds out not only did he knock her up, but refuses to take responsibility, the other girls refuse to have anything to do with him.
In the meantime, he's broken up with the first girl, but only after cheating on her for a long time. Said girl sinks into insanity and denial, especially since she knew he was cheating all along. Desperate after finding all his girls left him, he gets back together with the first girl, and tells the pregnant girl to get an abortion after making out with the other girl in front of her. Said girl later comes to his apartment and brutally murders him, the first girl sees the body, brutally murders her, and then leaves in a boat, cradling the guy's severed head in her arms, with a creepy smile on her face.
Also showed what kind of girls would be in an Unwanted Harem. At best needy, at worst psychotic. Kotonoha and Sekai particularly deconstruct Satellite Love Interest: they both lose what's left of their personalities to chase after Makoto... but this is done deliberately to show the terrible consequences.
The story also shows what could happen if someone really did treat a group of young women that all had feelings for him like your typical h-game player treats the female characters of a game, if some of those women happened to be extremely unstable. Most real people wouldn't react like that, some would. It also makes it clear that someone pursuing solely his or her own pleasure with everyone in sight while paying no attention to the effects that's having on others is an immature, maladjusted jerkass, and that such behavior can have terrible consequences.
Also brings up the true implications of the Lovable Sex Maniac / Bromantic Foil. Makoto's best friend Taisuke is a spirited yet hopeless romantic, and his perverted antics and subsequent rejections are portrayed as zany comic relief for most of the show. But then after being turned down once again on the day of the school festival, he resorts to actually raping a girl via taking advantage of her when she's at her lowest point; this not only throws the victim through the Despair Event Horizon, but it shows the character archetype to be much less harmless than commonly assumed.
Patlabor may be the ultimate deconstruction of the Mecha-genre: It has no superheroes nor supervillains and the mechas are plain and simply tools; the majority of them are used at construction sites and storages. They're anything but cool and if there's something even uncooler, that would be being a member of the Patlabor unit.
Mai-Hime functions as a fairly solid deconstruction of the Magical Girl genre, too, with the first half of the series being almost entirely fluffy, silly character-building and harmless Monster of the Week fighting (to further the point: the heroines battle a monster that steals lingerie), until around the halfway point when it decides to Get Serious.
Despite being the go-to "silly school comedy," School Rumble messes with the genre and deconstructs a surprising number of its tropes. Not only is the ditzy female protagonist we so often see replaced with a badass male delinquent, many situations are gender-flipped (such as when Eri walks in on Harima naked). Then, of course, there's the deconstructions of Clingy Jealous Girl (Eri nearly ruins her friendships when she thinks her friends are interested in Harima), Tsundere (Eri again, most people can't relate to her because she flips between extremes so much), and Yamato Nadeshiko (Yakumo's inability to confront people turns her into an Extreme Doormat who can't make friends).
Narutaru (Shadow Star) deconstructs the pet monster genre in a very disturbing and bloody way. To control their companions, the children have a psychic link with them which can take a heavy toll on both their body and mind, and some become very aware of the power they have and abuse it - even to the point of mass murder. The manga also looks at how the government and military might actually respond to Mons being involved in all manner of strange and violent circumstances, which leads to a lot of cover-ups and extreme measures.
Furthermore, the show deconstructs the "magical tournament/There Can Be Only One" type of anime as well: It's later revealed that the creatures the kids have been fighting are actually human pilots from parallel universes, specifically the battles are contests to determine which of the selected universes would be erased from existence. (Who is doing this and why has yet to be explained.) So the pilots have to choose between either winning the battles and dying or losing the battles and dooming their universes.
The author manages to one-up himself by explaining that even if the characters manages to make it through the requisite 14 battles and earn their universe's right to live (killing all of said characters in the process), it's not really over: the "system" that picks universes to fight might wrap around and choose the protagonists' again.
Originally, Super Dimension Fortress Macross was meant to be a Deconstructive Parody of shows like Mobile Suit Gundam. While it veered off that course eventually and played a fair number of tropes completely straight (never mind inventing a few along the way), pretty much every major entry into the franchise has featured at least one major, often scathing, deconstruction of the science fiction, adventure and anime genres.
Tsubasa Reservoir Chronicle starts out as a light-hearted True CompanionsGotta Catch 'Em All adventure story with some darkness around the edges and interesting sexual subtext. One-third of the way through, everything you thought you knew turns inside out and the most light-hearted elements become harbingers of the ugliest secrets. From there on out, the series proceeds to do everything it can to make your mind boggle, including introducing major unexpected Squick into what had once been CLAMP's most popular and innocent pairing.
The "Perfect GT-R" arc of Wangan Midnight has a beautiful deconstruction of street racing. Jun Kitami, who at this point has been portrayed as a reckless, heartless daredevil tuner, says point-blank that there are no winners or losers and that Koichi did exactly the right thing in giving up this senseless hobby so he could return to his wife. Given that the whole manga is about street racing, plainly admitting a truth like this took guts. Even better, this happens in the very first arc after the Devil Z and Blackbird are introduced.
Archer: There is nothing at the end of saving people.
Halo Legends is a deconstruction of the whole Halo series. The themes it presents are all present in the canon of the games, to a lesser extent, and the other supplemental material, to a greater extent, but Legends takes it to a different level.
In The Babysitter, it's showed that not all UNSC personnel are fond of the Spartans — some are actually jealous of them for their awesomeness, and they use it as an excuse to treat the Spartans as freaks, which has a bad effect on their cooperation. In the end, even a Super Soldier is a human being who can die just like that.
The Duel reveals that not all the Covenant believe in the "Great Journey"; some are to afraid to admit to it, some rebel against it and others just use the religion as a means for their own selfish needs.
Origins is a story about the Forerunners and their war against Flood. The message: no matter how powerful your empire is, it will sooner or later fall, especially if you fight against an enemy you don't have a single clue about.
Prototype deconstructs The Stoic. In this episode, the other marines believes that the main character's stoic personality is evidence that he's literally emotionless and that he doesn't give a damn about his fellow men, but contrary to their belief, he has as many emotions as they have, the stoicism just a facade to hide the pain that came from seeing his entire company being wiped out and having his last recruit bleed to death in his arms.
Toradora! deconstructs many of the character archetypes seen in typical Harem Anime. Most notably, Taiga basically answers the question of what kind of experiences could give a person a childish tsundere personality in real life: HUGE personal issues of the familiar kind, which also don't mesh well with the girl's own self-esteem problems.
Digimon Tamers deconstructs a number of things that were barely or not touched upon in the Digimon Adventure canon, such as the involvement of adults, how the government would react to programs emerging into the real world as monsters, how those programs came about in the first place, what a world governed only by the doctrine of "survival of the fittest" would be like (namely, harsh and unforgiving), how frustrating it is to be the Ineffectual Sympathetic Villain, and what would happen to a Tamer if their partner Digimon died. Later, the first arc of Digimon Savers could be seen as a deconstruction of part of the ending of Digimon Adventure 02, specifically the part where everyone in the world got a partner Digimon - it deals with the idea of those of dishonest intent using their Digimon for crimes, something Adventure 02 never even considered.
Probably the most telling part of Tamers being a deconstruction is the ending of the first episode. After Guilmon Bio-Emerges into the Real World, Takato is ecstatic to finally have his own real Digimon. And then Guilmon shoots fire out of his mouth, causing a huge explosion. It's at this point that Takato realizes that what's in front of him isn't just a virtual pet; it's a digital MONSTER, now allowed to roam reality. Production notes for the series show that one of the goals of Tamers was to (re)establish the fact that Digimon are, in the end, feral beasts who live to battle, and Guilmon's introduction nails it.
Maria†Holic is this to the Yuri Genre, alternating between cruelly subverting and playfully mocking tropes associated with it through the wacky hijinks of the Genre Blind schoolgirl Kanako Miyamae and her "ideal girl" Mariya Shidou... who's actually a Creepy Crossdresser.
Puella Magi Madoka Magica is, for the majority of the series, a pretty thorough deconstruction of the Magical Girl genre. The premise starts simple. Young Naïve Everygirl Madoka and her Wide-Eyed Idealist friend Sayaka, are approached by Mentor Mascot Kyubey, and the relative Cool Big Sis Mami, where they are given the opportunity to become Magical Girls. In exchange, they are granted one wish, that can be anything they want, but they will have to fight demonic entities called witches for the rest of their lives. In addition, a Dark Magical Girl, Homura, is opposed to this, and is constantly trying to prevent the two from making a contract. Sounds reasonable enough. Then the show demonstrates exactly what happens to those young girls who are forced into fighting Eldritch Abominations with no chance at a normal life.
Mami is ultimately an extremely lonely Stepford Smiler who is broken on the inside due to losing her parents, and being forced to fight with no real friends. When Madoka does become her friend, her subsequent joy leads to her death, and also reminds us that these encounters are far more dangerous when removed from the sweet and innocent flavor that permeates most Magical Girl shows.
Sayaka decides to use a Selfless Wish to heal her crush, Kyousuke, much like any typical superhero but as the other characters demonstrate, there is no such thing as a Selfless Wish, as they all have a selfish intention. In Sayaka's case, it was so that she could get together with Kyousuke, and when he doesn't return her affections, she breaks down.
Kyubey shows exactly what kind of "mentor" would knowingly send girls off to their death, without giving the full details, and more importantly why he would that - it's revealed that he's really more of a magical girl villain that sets up magical girls to turn into the very monsters they fight so he can harvest their energy. Even that is played with since he's gathering that energy to stave off the heat death of the universe.
At the end, however, Madoka becomes a Magical Girl, and uses a Cosmic Retcon to make it so that Magical Girls will not become witches. Although Magical Girls will have to fight demons /wraiths instead of witches, it is implied that the situation is better than before but still realistic given the new premise.
Several chapters of Franken Fran deconstruct the Toku genre, what with some of the Sentinels using their fame to become rich with merchandising, blackmailing influential people to get more funds, one becoming addicted to fighting to the point that he can't have an erection otherwise (leading him to set up people to get killed just so he can avenge their death), the families of the faceless minions killed by the Sentinels teaming up to avenge their deaths, and the evil organisation's Evil Plan being to cure all illnesses, stop famine, and create hospitals for everybody.
While the series itself isn't entirely a deconstruction, Mahou Sensei Negima! does deconstruct a few individual plot points common to shounen:
Negi's Training from Hell, while played straight at first, is shown to be extremely emotionally and physically draining on him, and it takes a toll on his relationship with his students.
Negi's father is basically one long Deconstruction of the Boring Invincible Hero / Idiot Hero archetype. He's an extremely powerful fighter, yes, but his tendency to never use his brain results in his plan ultimately failing. Basically, because Nagi just charged in to punch bad guys before figuring out what was actually going on, he wasn't able to actually fix the real problem. Ultimately, Negi, who's not an Idiot Hero and actually takes the time to analyze the situation and work out a workable solution, is the one who really fixes things as opposed to just delaying them a bit.
Bokura no Hentai deconstructs the Otokonoko Genre. At first glance it seems to be a standard tale about three crossdressing tweens but it gets Darker and Edgier after the first chapter. The series goes on to show how Growing Up Sucks and subverts many tropes, such as cruelly averting It's Okay If It's You by having Shuu's reason for crossdressing being that he's in love with a straight boy. Said boy is homophobic and will only sleep with Shuu if he's dressed as a girl. He's abusive towards Shuu and he helps awaken sex-related issues in Shuu.