When done right, a dark ending where overpowered villains are successful can be incredible. It can hit the final note of what was a bleak story up to that point or give a bittersweet style ending where the villain gets what he wants, even as the hero is victorious. In a world where the hero always wins, it's such a nice change of pace.
One of the few genres willing to take the risk is the shonen genre, especially when the series has a charismatic lead villain. It doesn't always hit, but you have to respect an anime that takes the risk.
10 Neon Genesis Evangelion Ends With The Human Instrumentality Project Starting
There's a reason for the critical acclaim the series got, and a big factor in why is it wasn't afraid to take risks with its story. One of those risks was having Seele, the mysterious cabal that pulled the strings behind the scenes, still achieve their goal by triggering the Human Instrumentality Project. It was one of the risks that wasn't as well-received by everyone, the finale being highly derisive.
9 Devilman Crybaby Ends With The Entire World Being Obliterated
The name doesn't do the anime justice. With a name like Devilman Crybaby, you'd expect something that was more of a comedy than what's offered. It's a bleak anime that doesn't hold back, never even giving you a hint that it's going to end happily. Even that doesn't prepare you for what's one of the darker endings in an anime where not only does the hero fail, but the entire world ends up getting destroyed after God cleans up the hell unleashed on earth.
8 Yu Yu Hakusho Ends With Sensui Getting His Wish Of Dying To A Demon
The end of Yu Yu Hakusho is one where everyone comes out on top. Sensui was one of those villains whose end goal was death, much like how the Joker would win if he ever got Batman to kill him, the same held true here.
He wanted to fight a person strong enough to kill him, one that Yusuke can give him. Their fight is bitter-sweet in that way as Sensui thanks Yusuke for letting him enjoy fighting for a brief moment before passing on.
7 Berserk Ends With Griffith Becoming Femto
The 1997 anime adaptation ends with Griffith achieving complete and total victory. He becomes the fifth member of the Godhand, casting aside any bonds he once had with his friends. It's one of the best betrayals in anime and one of the most brutal. The things he does to his former friends, mainly Casca, are beyond comprehension and paint him as the ultimate evil. While the manga is continuing on past that point, the anime ends there, and most adaptations conclude with him winning in some way.
6 Fairy Tail Ends With Zeref Breaking His Curse
Admittedly, this is one of the least conventional moments of a villain winning, but that's because Zeref wasn't necessarily the villain he was made out to be at the start of the series. He certainly did bad things, but once you find out his backstory, it's hard not to want to see him succeed. By the end, that's exactly what happens, albeit under different circumstances than he expected. Acnologia is defeated, and his curse is lifted, allowing him to live his life with his true love, Mavis.
5 Mobile Suit Gundam: Iron-Blood Orphans Ends With Rustal Elion At The Head Of A Reformed Gjallarhorn
There were some shades of grey in play, as they're often are with Gundam villains, but it's pretty clear that the Gjallarhorn were the bad guys in the situation. It's what makes the ending so surprising as Rustal Elion, the primary antagonist, gets everything he wanted by the end of season 2.
He wipes out Mcgillis's fleet, ends Tekkadan as an organization, and reforms the Gjallarhorn into a Democratic organization. Naturally, this all earns him quite a bit of fame and renown.
4 Part 1 Of Naruto Ends With Orochimaru Getting Sasuke
While not necessarily the end of the series as a whole, Part 1 and Shippuden feel like separate entities due to the time skip. In Part 1, the entire plotline revolved mostly around Sasuke's need for revenge and Naruto's desire to change his mind. That ended up carrying through the series in a greater scope in Part 2, with Naruto succeeding. However, he failed in Part 1, being unable to rescue Sasuke from the clutches of Orochimaru's influence.
3 Mobile Suit Gundam Wing Ends With Treize Getting Everything He Wanted
Treize is one of the better villains in Gundam, a series that's chock full of them. He's an extremist, as many of the villains in Gundam are, but he's well-intentioned in his goals. Yes, he wanted to start a war larger and more destructive than seen prior, but only because he felt it was the only way to make the people more receptive to peace. He managed to pull that off and did it all while achieving his secondary goal of dying in combat.
2 Hellsing Ultimate Ends With The Major Completing His War & Defeating Alucard
By the end of the series, The Major had started his great war and managed to defeat Alucard in the most convoluted fashion. It didn't matter that Integra ended up killing him in the end or that she called him a monster for becoming more machine than man. He'd achieved everything he set out to do. Some of this ends up subverted as Alucard does end up coming back to life, but it doesn't change that The Major got what he wanted.
1 Speed Grapher Ends With Suitengu Plunging Japan Into Economic Crisis
Of all the villains who've come out on top in shonen, none have as resounding a victory as Suitengu. He gathers all of the yen in Japan into one building, a building that also holds the Ropongi club. With everything he needed under one roof, he detonates a bomb, killing him and everything else with him. If that weren't enough, he also manages to permanently blind his rival, Saiga, due to overuse of his power. It's a pure and total victory for Suitengu.