I'd say the only real main villain (through and through) is Orochimaru (with the exception of some of the former Akatsuki members who chose to walk the dark path out of their own free will).
Madara, Obito, Kabuto, Nagato (Pein), who although have all (and some currently still) walked the path as villain, were all backed into that corner and chose that path as a result of some trauma or pain. Drawing their own conclusions and validating their reasons for their actions.
Orochimaru on the other hand chose the path of being villain simply because of his own greed, lust, and jealousy. Greed: his hunger for power. Lust: his desire to acquire Sasukes body and the power of the Sharingan. Jealousy: His anger at Hiruzen Sarutobis decision not to make him Fourth Hokage, in which Minato was chosen instead of him. These feelings, as well as his complete disregard for human life (kidnapping, murdering, experimenting on his own people, etc) make him the most consistent and believable villain as there is no sad story behind it; only his selfish lust for power.
That and the fact that he was villain from the beginning and has made it this far, as well as the fact that his Snake like persona makes him even more untrustwothy. I have no doubt that even at this stage in the Manga, that It's possible he has a plan.
So my answer (obviously) is Orochimaru. Although, granted, there have been many and are many who have played the part of 'villain'.
