A good villain can make or break a shonen series. Their goals, their abilities and how much of the audience sees them is vital for building them up as legitimate threats. Yoshihiro Togashi, author of Yu Yu Hakusho and Hunter x Hunter, handles his villains a bit differently than your typical shonen, especially in the later series.
The villains of Hunter x Hunter are more like chaotic entities. Let's look at The Magician Hisoka as an example. He doesn't have any long term goals for obtaining power, wealth or status; all Hisoka wants is to find fighters with overwhelming strength in order to fight them. When Hisoka first encounters Gon during the Hunter Exam, he doesn't kill his opponent even though he could have. Instead, Hisoka let Gon live because he saw his potential and wanted to see what kind of fruit he'd bear when the young hunter ripened. Hisoka can play as either an ally or enemy depending on the specifics of a given situation, and what he thinks will be the most fun.
This becomes even more intriguing when Hisoka helps Gon and Killua become stronger in his own strange way during the Heaven's Arena arc. Hisoka won't allow the two boys to advance to their next fights unless they can successfully pass through his Nen field without hurting themselves. Because of Hisoka's twisted obsession with combat, Togashi is able to play him into several different situations that not only fit his character but keep the reader surprised and intrigued. This is especially true with his relationship with the Phantom Troupe and Chrollo Lucifer.
The Phantom Troupe is a group foreshadowed very early on in Hunter x Hunter. They're a gang of thieves who steal anything valuable that catches their radar, most notably, the scarlet eyes of Kurapika's clan. They're built up as a soulless and bloodthirsty group that leaves nothing but corpses in their path. However, when we finally meet The Phantom Troupe at the beginning of the York New City Arc, that's not really what we're introduced to. The Troupe talks and acts like a group of friends who've known each other all their lives. On the way to the city, two members, Franklin and Nobunaga, get into a fight about something completely pointless the way friends do. When the group gets ambushed by the mafia, one of them fights and says not to interfere while the rest sit back and play cards.
Later, when Shalnark finds the chain user's identity for Uvogin, the buff and masculine Uvogin kisses Shalnark on the cheek in complete sincerity. It's honestly a really sweet and cute moment. When one of their members later dies, none of them see it as that character being weak; Nobunaga breaks into tears over losing his best friend. The troupe may be merciless killers, but they look after each the way a family does. In a very strange way, it endears you to these villains in a way few anime manage to do with even their heroic characters. The Troupe members have a human side to them we don't see in a lot of shonen villains, and this is especially true for the leader Chrollo.
In a 2013 interview in Hunter x Hunter Vol. 0, Togashi talked about why he liked Chrollo as a character said because "Chrollo isn't a leader who nominated himself." Togashi seems to dislike people who nominate themselves as if they're the answer, so he wrote one of his main villains without that quality. Chrollo will often put the Troupe before himself, best seen in the sacrifice of his Nen powers to Kurapika to save Paku's life. The only reason Hisoka even joined the Phantom Troupe was so that he could fight Chrollo one-on-one at some point, something that Chrollo was always prepared for, but took the risk because of how useful an asset Hisoka is.
Togashi would later write the exact opposite sort of villain with Pariston. During the 13th Hunter Chairman Election Arc, Pariston is the first person to outright nominate himself as the new chairman, to the annoyance and detriment of the rest of the Zodiac. Pariston's coy smile, sly personality and laid back attitude make him the most disliked member of the Zodiac. He's very unpredictable which makes him hard to deal with especially because he seems to only be interested in making things entertaining for himself. But he's not out to maliciously become the new chairman or make the Hunter Organization in his image. It's that kind of offbeat type way that Togashi writes his villains that make them so interesting to dissect and still keep Hunter x Hunter interesting so many years later.
In another interview with One Piece creator Eiichiro Oda, Togashi also talked about his dislike of convention and following a "predefined scheme." This shines through in nearly every arc of Hunter x Hunter, specifically in how the plot will move forward in a way that constantly catches the audience off guard. Togashi can convincingly shape protagonists like Kurapika and Gon as terrifying villains. During the York New City Arc, Kurapika is hyper determined to find and get revenge on the Phantom Troupe that slaughtered his clan. To do that, he goes on a warpath with no room for mercy or sympathy for the people who don't even remember the day they destroyed his life. In this sense, Kurapika is now framed as an antagonist to the Phantom Troupe, and we're inclined to root for The Troupe because of how well Togashi writes them as believable human characters. Kurapika was always a heavier burden then he let on, so this isn't out of leftfield for him. Rather, we're seeing a side of him he rarely let slip in front of Gon, Killua and Leorio.
Togashi doesn't write his villains to be disposable or ways to make his heroes more heroic by comparison. These are characters who have just as much agency and thought put into them as Gon or Killua. It's that kind of consideration that makes Hunter x Hunter still just as relevant as ever.
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