Ghetsis from Pokemon Black/White Generation. No other leader of any of the other opposing teams in generations past have ever made me legitimately hate them because, like it or not, they were at LEAST honest in their beliefs. Ghetsis, on the other hand, was a total lying manipulative scumbag, manipulating both the general population AND a good portion of Team Plasma into thinking they were doing the world a good thing by separating people from their Pokemon. Pokemon Liberation, as they called it (think "Animal Liberation" ala PETA). In actuality, this was all a ruse so that Ghetsis and Ghetsis alone could wield the power of Pokemon and rule over the Unova Region.
That sort of thing REALLY pissed me off. That and his Hydreigon, but mostly that other stuff.
It was kind of a surprise to me that the whole "pokemon liberation" thing was a huge lie and that he really just wanted to be the only one with pokemon so he could rule Unova, which really made me kind of hate him.
Also, he's not much better in B2/W2. His plan there is to use Kyurem's power to freeze Unova. Really? Freeze Unova? How much would that really accomplish?