Just because an anime character happens to be the protagonist of a show doesn't mean they’re the most interesting person to focus on. Sometimes the most fascinating character is a compelling villain, the one trying to upset the status quo by introducing some calculated destruction.
Some series have a multitude of horrifying anime villains, and it’s hard for the protagonist to even compare. Naruto turned Itachi Uchiha from a blood-thirsty villain into one of the most empathetic characters in anime history. Let's be real, Naruto Uzumaki has nothing on Itachi.
Other times, a single villain makes a more memorable impression than the main characters - Dilandau’s arc in Escaflowne is far more dramatic than Hitomi’s.
It’s not that these protagonists are bad, it’s just that the villains are better.
Hunter X Hunter has an excellent cast of characters, so it's a wonder that the villains can sometimes outshine the already pretty cool protagonists. Gon is in some ways a typical shonen protagonist, but he's also better at strategizing than most. He can be easy to ignore, however, when Hisoka Morow is around.
Hisoka is a fantastic villain because he's so absurdly evil that it's hard to feel any emotions about him other than stunned. He's completely lacking in compassion for other people and will readily betray former allies if he thinks it will be more entertaining to do so. Sure, it's great to have villains with consciences, but it's also nice to have villains that revel in pure evil.
On the flip side, there's Mereum, a Chimera Ant who starts out just as arrogant and cruel as Hisoka, but who forges a friendship with a young blind girl named Komugi. He dies before he ever has the chance to fully redeem himself, but his transition from a selfish person to someone with compassion and empathy is wonderful.
Naruto Uzumaki is a typical shonen protagonist. This isn't inherently bad, and both the character and his series did help to define the genre. Nevertheless, Naruto is far from the most fascinating character in the anime.
The villains in Naruto do some reprehensible things, but they are fascinating figures nonetheless. They're presented as fully-formed individuals with a range of motivations, which makes it easy for viewers to empathize with them. Few people can hear the full explanation for Itachi killing off the members of his clan without understanding his motives.
Meanwhile, it's hard not to loathe the villain who put him up to it, Danzo - while simultaneously being fascinated by his role in Konoha's complex political system. Madara is breathtakingly cruel, but also hard not to admire for his sheer power, as well as his ability to transcend human limitations.
Nearly every villain is far more interesting than Naruto, and the show could be improved by spending more time on them.
Though the DBZ fandom's affection for Goku is somewhat deserved, he's far from the best thing about the series. That's because he doesn't undergo a whole lot of character development over the course of the series.
His cheerful, competitive, and clueless personality remains roughly the same from start to finish, even though he's had plenty of meaningful experiences - including his own death - that ought to have changed him a little.
The show's cast of villains is a lot more interesting - especially Vegeta. Vegeta goes from being a hardened murderer with no empathy for others, to someone who is committed to serving others and bettering himself - all while maintaining the basic core of his original personality.
That transformation is fascinating because it constitutes genuine character development, inspired by the plot. Goku will always be Goku, and while that's not inherently bad, he just not as engaging as Vegeta.
There's some debate in the Durarara!! fandom about whether the true protagonist is Mikado Ryūgamine or Celty Sturluson, but most tend to go with Mikado.
Mikado isn't a boring character, but many people would call Izaya Orihara their favorite. Izaya is an underground information broker who loves manipulating other people in order to test their reactions and learn about the human race, which he claims to love.
Both hilarious and mysterious, Izaya makes a major impact on the show that the naive Mikado, whose goal is to make his own life less boring, can't really hope to compete with.