Oof, this IS a tough choice, what with all the great villains around. Ghirahim nailed Ghetsis on the head there, as he's the ONLY villain in all the Pokemon games that I actually truly hated because of his character. I mean, sure, the other teams WERE a bunch of villainous jerks. But, despite their rotten intentions, they actually BELIEVED in what they were doing. Ghetsis, on the other hand, was simply using ALL of Team Plasma to further his own agenda, that being becoming the only individual in the Unova region to be able to use Pokemon, thus solidifying his absolute power and domination over that section of the world.
What a bastard!
But, since Ghetsis has already been covered... I'll go and throw Luca Blight's hat into the ring. My GOD was this SOB evil. He was rotten to the core, chopping down men, women, and children who got in his way. He would even have people beg for their lives by acting like pigs, only to cut them down soon afterwards after they had amused him. But even then, despite all the evil he's done, you DO feel a bit sorry for him after learning what made him so mad. I mean, witnessing your mother get assaulted by brigands while your father ran away with his tail between his legs as a young boy WOULD screw you up mentally, I would think. Not only that, he has to live with an ETERNAL REMINDER of that horrific incident what with the existence of his half-sister Jilia, who was conceived as a result of that attack.
To give you an idea as to how bad Luca Blight was, the mission in Suikoden 2 where you finally kill him was only possible because of a secret joint operation with the ENEMY SIDE. He was SO BAD that even THEY did not want him!