This is an odd one for me because if I'm being honest I don't think Shonen Anime has a history of great villains. Plenty of good villains, but not many that I think are truly great. There exist a few exceptions, but most Shonen it gets by on great action and protagonists. I love me some Dragon Ball Z, and there were a lot of good villains there, but even the best of them just don't compare with someone like Johan from Monster, or Vicious from Cowboy Bebop. A few I'm still behind on, like One Piece and Hunter x Hunter, but this is largely not a genre I feel is known for great villains.
Of course, this also comes down to how loosely you define Shonen Anime. While I think most fans look at the term and have an idea, I don't know if there is way I hear it used (At least not here in the west) that makes it entirely clear. Just to make sure, I used this list to personally determine if what I was looking at was Shonen or not.
That said, it isn't to say that Shonen doesn't have a handful of truly great villains. I fairly quickly came up with four contenders, and I'll first go over the three that didn't cut for me. I will say right now though, my actual pick for best villain of Shonen is going to be a spoiler, as I cannot even discuss the villain in any detail without revealing a huge twist of the anime it comes from. I'll name the anime before revealing the villain I refer to, so anyone who has not seen it and wants to can leave this article without the spoiler.
The first cut I made was Tsukasa from Dr. Stone. I kind of feel this show is too new to honestly give him that reward, as time tends to adjust how one feels about certain shows. Kaguya just plays wonderfully as the Pragmatic villain faced off against Senku as an idealistic scientist. I love that the typical way these roles are portrayed is reversed here, and the rivalry works so well because neither of them is evil people, they both want to save the world, their methods just clash.
The next two cuts were both from Jojo's, and at first, I thought I was going to select Dio as my number one pick. Kira was also a fantastic villain. His solitary lifestyle was a perfect foil to the themes of community that the fourth part of Jojo focused on. His powers were crazy and fun, creating so many interesting fights and situations. Dio, however, may be one of anime's greatest villains that are fairly shallow. There is some depth in the beginning as Dio forsakes his humanity, but what sells it is after he does that it truly does feel like he's become something far beyond human. He may not have a deep character at all after that transformation, but he has a presence about him that makes him feel so much more than anyone else, he's an intimidating figure. Sadly, he doesn't quite make the cut either.
The Show I'll be talking about now is Psycho-Pass. If you have not finished at least the first season, step away from the review now because I am ruining one truly fantastic twist.
My selection best Villain in any Shonen Anime isn't typically who you would think of as the 'Villain' of the show, or in the case of Psycho-Pass the villain of either season one, two, or three. It's a show where the lead antagonist changes each season. That said, this is best Shonen 'Villain' and not Antagonist. Frankly, depending on the circumstances, the best villain of Psycho-Pass isn't necessarily the Antagonist, it's the ever-present Sibyl System.
Originally described as an AI, the Sibyl System is effectively in control of all Japan. It can approve career choices, it meddles in elections, and most importantly it determines a person's Crime Coefficient. This is a numerical value the system gives out based on a person's mental state and determines the likelihood of a person committing a crime. Even the actions of law enforcement are bound by their target's crime coefficient. This leads to the first antagonist of Psycho-Pass, Makashima. He is what the show calls' Criminaly Asymptomatic'. No matter what he does, even if he is in the act of killing another human being, his Psycho-Pass remains clear. The weapons used by the police read his psycho-pass, and as a result, are unable to fire.
Makashima himself isn't the focus of this article, but this is where you start to see doubt about the Sibyl system form in the mind of Akane as to what Sibyl is and how it works. No one actually knows how Sibyl makes its determinations. Eventually, Akane learns to truth, Sibyl is not an AI, but a collection of human brains that have been linked together to act as a sort of supercomputer. Specifically, the system used the minds of criminals in order to determine the likelihood of its targets being criminal. Occasionally, when the asymptomatic appear, Sibyl uses its officers to capture the target alive and add their mind to the system, thus increasing its ability to determine one's crime coefficient. Because of the criminal influence in the system, it doesn't always operate in the most savory of ways.
The truly sinister thing about Sibyl is this system pretty much runs and operates in Japan with the full blessing of the majority of the population. Shutting it down or exposing it isn't an option, people have largely just become complacent under the ever-watchful and protecting eye of big brother. Security vs Freedom, that is the real conflict of Psycho-Pass. The truly sinister thing, however, is the protagonists never really have a choice but to work with Sibyl.
There is no getting around the fact Sibyl rules by stripping as much choice of the population as it can, and all the antagonists of the show exist as a direct result of this. But to simply eliminate Sibyl would undoubtedly bring about an end to the society of Japan, and considering the state of the world outside that would cause catastrophic damage to them. It's a villain you can't defeat without what amounts to a Pyrrhic Victory.
And Akane realizes this, and while working with Sybil is doing what she kind to try to change the system as well as trying to get society to a point they may be able to break free of Sibyl without collapse. Where this dynamic is so interesting is both Akane and Sybil know that their views on the world are incompatible, but they have no choice but to work together. Akane, despite having had opportunities to get rid of Sybil, has actively protected it instead. Sibyl, on the other hand, has no way of passing judgment on Akane because her Crime Coefficient never raises (I suspect she may be Criminally Asymptomatic, but the show never confirms). It's one of the most interesting dynamics I've seen in an anime for a long time.
In the case of Sibyl, the show is painting this as a horrible thing. Every moral dilemma, every antagonist, and even most of the protagonist's obstacles all originate from Sibyl. On the other, while at odds for periods at a time, by and large Akane works with Sibyl against the same antagonists of the show. I may be stretching the term 'Villain' a little bit here. Regardless, Sibyl is one of my favorite elements of any anime, and this show is definitely worth a watch. I'm a bit hesitant to recommend the third season (The first two work as stand-alone stories, so you don't need to watch past them) until season four comes out, as it's the first time two seasons directly connect the story like this.