Oh sure Hajime isn't a villain, but that's more because of extended use of the Human Undead by Joker to assume a human form as he hunts down the other Undead to accomplish his goal of "Win so everything can die." Every use resulted in Human affecting Joker more and more and eventually the Joker Undead gained a kind of humanity that made him cherish those humans living, like Amane-chan. Annoying as she could be at times. But in the end, Joker, long prior to Blade and use of the Spirit Human Rouze Card, was indeed a very powerful villain.

Probably the Overlord of Darkness, what with him being effectively God.

N Daguva Zeba is also pretty scary in theory, although we never really get a good sense of what he can actually do.

As much as I hate this, the Shadow moon that fought Decade and his pet Kuuga (who was Super-Ultimate or whatever) is a good contender, as he beat back the supposedly final form of Kuuga, and Decade who apparently can take on all past Riders.

Roshuo because godlike abilities and he obliterated Kaito and Kouta easily. Heart because of the dead zone and his super evolution. I would also give the third place to Upgraded Sagittarius zodiarts.