Magnificent Bastard/Multimedia/Pokémon

The magnificent masterminds of the Pokémon franchise:

Games

 * Team Rocket's boss Giovanni is the quintessential villain in the franchise. He has been portrayed as this trope in adaptations, and his gameverse incarnation is still dangerously clever. Whether it's running illegal operations right under everyone's noses in Celadon City, taking over Silph Co, or killing Pokémon for profit, Giovanni oversees all sorts of evil schemes while acting as the legitimate Gym Leader of Viridian City, a title he abdicates out of respect for Red once he's beaten for his badge. Then there's the version of him that leads Team Rainbow Rocket, an evil team made up of the series' previous evil team leaders from alternate universes where they won, who takes over Aether Paradise in Ultra Sun and Moon and nearly takes over the multiverse. While his plans are never as destructive as the villains who would come after him, Giovanni is easily the coolest, craftiest of the bunch thanks to his strong, if warped sense of honor, and tendency to slip back into the shadows when his plans go belly-up.
 * The core game series also has Cyrus, Big Bad of the Generation IV games and boss of Team Galactic. He's shown to always be steps ahead of you or the other good guy characters, has an intricate criminal/terrorist operation carried out while using his team doing official business for his energy company as a front for these crimes, is highly intelligent and calculating, and has enough charisma to sway the spirits of his followers and deceive them into following his stated cause of using the powers of time/space to Take Over the World and change it for the better, when in reality he plans to literally destroy the existing world with these powers and create a new one where all living things would be stripped of spirit and he'd reign over it as God of a new universe. As a master of suppressing his emotions, he rarely ever loses composure and is strangely respectful and courteous towards his enemies too. Unlike other villains, he claims to not use Pokemon as friends or tools, but instead make their power his own through his man-made devices fueled by their energy such as the Red Chain. Cyrus ends up being so magnificent that even his enemies grudgingly respect him, and even when his plans are shot to hell, he walks off with the ominous warning that he will never stop working towards his ultimate goal: a world without spirit.
 * in Pokémon Black and White not only attempts to separate people and Pokemon forever, but He's a masterful example of Dangerously Genre Savvy, well aware of the importace of Pokemon, and is perfectly prepared
 * It should be noted that he's a rare example of what makes him such a magnificent and skilled bastard also makes him completely evil.
 * Also, while his planning skills may be worthy of being called magnficent, his overconfident, pompous attitude...is not.
 * Colress is a straighter example in the sense that while he's just as intelligent and devious as his boss, completely succeeding in freezing Opelucid City and overseeing Neo Team Plasma's actions, he takes his defeats a lot better and manages to turn over a new leaf as well.
 * In Pokemon Conquest, it goes without saying that Oda freaking Nobunaga himself counts. The man's audacious enough to try to kill Arceus in a bid to end all wars, and manages to trick the heroes into opening themselves up for a surprise attack after pretending to lose to them, while also tricking them into summoning Arceus so he can kill him. Definitely a lot more kid-friendly than most examples of this legendary warlord, but just as much of a tactical mastermind as the rest of them.

Anime

 * Giovanni, boss of Team Rocket, is less a mafioso/yakuza boss and more of a freaking Bond villain, and has access to a plethora of destructive giant robots, dangerous Pokémon catching gadgets, and has dabbled in trying to use Legendary Pokémon to do his bidding, such as the Genie trio and Mewtwo. And despite Jesse, James, and Meowth's constant blunders, he's always willing to give them a second chance since they never truly inconvenience him in the long run. And since he's been in charge of Team Rocket for the entirely of the series, it's safe to say that he's mae the right call.
 * Team Rocket's Meowth, of all people, attempts to be this in the Best Wishes series. During the journey to Nimbasa City, he played the gang like a fiddle by pretending to be fired from Team Rocket and wanting to join with them instead, and nearly got away with their Pokemon along with the other members of Team Rocket (Jessie, James, and Dr. Zager), who were all operating a surprisingly well thought out plan. Unfortunately for them, it's another situation where Failure Is the Only Option.
 * Dr. Colress, acting leader of Team Plasma in the "Episode N" arc of the same series, matches Meowth in charm and efficiently quick thinking as he was able to play off of his overconfidence to dupe him into becoming his test subject to use against Team Rocket. Unlike the rest of Team Plasma who seek to control Pokemon for World Domination, Colress is in it purely For Science!, having no true respect for Team Plasma's leader Ghetsis (he does not speak to him with the same reverence as his grunts do), constantly thinking well ahead of anyone else he may be sharing space with, and always advancing his technology so that he could better control the minds and hearts of Pokemon in order to strengthen them beyond their limits, even Legendaries like Reshiram. And he did all this in his own style with a perky, exuberant attitude towards his work, not minding at all that he was taking an amoral approach to bring out the full strength of Pokemon because he justified it as being in the Pokemons' best interest as well. Even in the end, the guy doesn't let crushing failure (and going to jail) get him down: he just vows to move on to a new approach!
 * Lysandre from the XY&Z series is no slouch either. The CEO of Lysandre Labs and secret leader of Team Flare, he tricks Alain into retrieving Mega Evolution Energy and an ancient stone he needs for his plans to revitalize the Kalos region, roping along Hoenn Champion Steven Stone while doing it to battle some out of control Legendary Pokémon, and for most of his tenure in the main series he's a Villain with Good Publicity of the highest order. By the time he finally executes his scheme, not only is everyone caught by complete surprise, but when an organized resistance composed of Ash's group, Alain, the Kalos Gym leaders, one of his own followers, and not one but two Champions oppose him, he turns out to be Crazy Prepared and has several solid contingencies in place. He didn't see Zygarde having another transformation coming, though.
 * Let's not forget Mewtwo's original persona from Pokémon: The First Movie. Let's see. Tries to Take Over the World (or just mass produce a whole race of Clone Pokémon to prove their superiority to naturally born Pokémon in the original version) in an outrageously audacious fashion, is almost never seen to lose his cool (and regains it pretty quickly once it's lost), quite the planner, charming in a calculating, suave kind of way, and, let's face it, was going to win until Mew showed up.

Manga

 * Pokémon Special:
 * Giovanni, boss of Team Rocket, manipulated nearly every event in the first Chapter of the manga via a huge criminal operation carried out under the guise of a string of seemingly unrelated incidents, had many plans (Mewtwo, the Legendary birds, the raid of Silph Co.) running simultaneously and even being altered to accommodate circumstances, and is shown to be so skilled at Pokemon battle that he can anticipate what his opponents' Pokemon will be, what move they'll make, what counterattack to use, AND how many seconds or minutes it all will take, all before anything's even happened yet, all with a suaveness, dignity, and imposing demeanor of a Diabolical Mastermind Yakuza boss. Subsequent appearances reinforce how magnificent a bastard, and what a surprisingly good sport, he is. Given he's been a trainer for YEARS, and, it makes sense. It also makes him a poster-boy (man?) for this trope here in this manga more than ever when compared to even the games and the anime.
 * Green also demonstrates aspects of this, despite being a heroine, particularly in the Red/Blue/Green Chapter and the Yellow Chapter, where she can best be called a Junior version of Fujiko Mine. A wayward thief and a con artist when Red first meets her, Green scams him out of his money by selling him an assortment of items that don't work properly, playing to his good nature in order to do so, and when he chases her down to retrieve his money and she finds emotionally manipulating him a second time doesn't work, she feigns falling unconscious to keep Red from noticing her swiping his two Gym Badges through sleight-of-hand. Using the badges to strengthen her own Pokemon, Green goes on to make fools of Team Rocket by stealing an important disc about Mew from them and constantly giving them the slip through clever trickery, even getting Red to help her out. Afterwards she seems to return his badges to him while she goes off to sell photographic evidence of Mew she got to tabloids...only for it to later be revealed that the badges she "returned" were fakes and she's still been holding onto the real ones for future use. During the battle at Silph Co., Green employs underhanded tactics to blindside Team Rocket's Sabrina and goads both Red and Blue into doing most of the heavy lifting for her so that she might claim the greatest prize in the end. Her strong showing at the Indigo Plateau Tournament gets Professor Oak to allow her the official runner-up status after he drops out. She then engineers nearly every event in the Yellow Chapter by setting Yellow on her quest and telling her never to remove her hat, which she bugs with a GPS beacon and recording device ("I've been... um... using Yellow as my learning aid!"), and also keeps Yellow wearing the hat so that Red remains under the impression that Yellow is a boy just for her own amusement to see how long it takes before he finds out the truth. When going up against Lorelei of the Elite Four, Green bests her through pulling a Batman Gambit where Even the Gold/Silver/Crystal Chapter has her showing an epic case of Crazy Prepared when  While she develops into a more straight-up Guile Heroine as she matures, the sneaky, mischievous qualities that made Green such a cunning and formidable opponent never really leave her.
 * The Masked Man/Mask Of Ice, is the Big Bad of the Gold, Silver, and Crystal Chapter. A malevolent and eerie yet well spoken figure always hiding his face behind a mask, he controlled the Legendary Pokemon Ho-Oh to abduct six children that he took in as his own and raised to be criminals, and while the youngest of these (Green and Silver) managed to escape him and become regular, if not still thieving, trainers, the Masked Man used the other four to gain influence within Team Rocket and the Pokemon League respectively without anyone realizing it. Brainwashing remnant members of Team Rocket with Mind Control masks and using to influence events, including funding a program that forces strength-boosting evolution upon weaker Pokemon, the Masked Man set his sights on the realization of a master plan years in the making that would gain him control of Celebi, thus allow him the power to control time itself. He came just an inch of success in the end, risking sending the entire planet through a Time Crash just so that he could  Despite being a Misanthrope Supreme who deployed cruel methods and almost wrought irreparable damage upon the world,  was a firm believer in loving Pokemon and doing anything you could for the sake of that love, and
 * The Black and White and Black 2 and White 2 Chapters features two leaders within Team Plasma, Ghetsis Harmonia and Colress, making their bids for this status, and as in the source material, Ghetsis ends up a subversion while Colress plays it straight. What's particularly impressive is that it's Ghetsis who carries the air of an polite, collected, calculating Chessmaster while Colress, according to Blake, is childish, emotionally driven, and "not mastermind material", yet Colress ends up proving the far more savvy, intuitive, and unpredictable of the two. First appearing under the guise of "Hoodman", Colress makes it clear that his loyalty to Team Plasma is based only in his desire to further his research on what draws out Pokemon's fullest strength. He uses his Ice Drive Genesect to freeze the Swords of Justice and obtains what he believes to be the Reveal Glass so that he can use it on the three legendary force of nature Pokemon when he sends them out to battle the international police and their allies at the Unova League. Finding that what he has isn't the original Reveal Glass, Colress is still able to amplify the Pokemon's power and overwhelm his opponents while he makes his escape on Genesect, on which he uses cloaking technology to hide it's form from any spectators. Two years later Colress spearheads Team Plasma's war on Unova, locating the runaway Sage Zinzolin to press him for information before taking him as a captive and using his Mind Control machine to subdue Kyurem so that it can be captured and it's power may be used to charge the Freeze Ray that's unleashed upon Unova, with Colress taking great glee in the results of Kyurem's full power on display. When Blake and Whitley infiltrate the Frigate, Colress is quick to intercept them and have them frozen and tossed down into the sea. Keeping in close contact with Ghetsis but beginning to tire of the back-and-fourths with his "friend" who he recognizes is only using him for his talents, Colress soon acts against Ghetsis' knowledge by rescuing N when Ghetsis attempts to have him killed, deeming N too valuable and extraordinary a person to be wasted, which ends up playing into Ghetsis' undoing. Amoral to a fault and dedicated only to his experiments and research yet also friendly and exuberant at almost all times, Colress believes that results justify the approaches taken to get them and proves smart enough to end up in a more well off position than his employer.
 * Team Flare's leader Lysandre in the XY/Z Chapter is also a strong qualifier. Like Giovanni and Cyrus he's suave, intelligent, stylish and ruthless, and like Ghetsis and Colress, has a back-up plan that he launches immediately once his initial master plan fails.
 * Pokémon Diamond and Pearl Adventure:
 * Cyrus, boss of Team Galactic, has some of the qualifications for this down. As in the games, he's a brilliant minded Visionary Villain who's often thinking many steps ahead of the heroes, is able to rationalize his actions no matter how deadly as being Necessarily Evil for the sake of a better future for the world, and has just enough charisma to sway many into following his lead without letting any of them know that he the plans to literally destroy the existing world with by resetting time back to the universe's beginning using Dialga's powers and then creating a new one in it's place where all living things would be stripped of emotion and free will, and he'd reign over it as it's God. Despite being notably more emotional and unhinged than his game counterpart, Cyrus possesses self awareness of his darkest emotions and this keeps him motivated in his ambitions to rewrite existence so that it may be rid of such emotions. His battle prowess and dedication to his cause consistently manages to impress Hareta despite him knowing that Cyrus is in the wrong, and Hareta in turn both impresses and influences Cyrus enough for him to rethink his evil ways. When Dialga and Palkia's fight threatens to tear apart all of existence, it's Cyrus who divulges a working strategy for stopping this from coming to pass, and when he returns to lead his old followers in the charge against Charon, they get behind him without question due to how bold and inspirational a leader he is, despite the fact that he'd previously mistreated or even tried to kill them!