Anarchy 2 - A political dissenter, this villian wants to change the system by completely destroying it, and he has very concrete ideas about what will come after - not rarely, installing himself on the top, or someone close to him. Or believes the anarchy itself will make all things right.
Sado/Masochist 2 - sexual tones aside, this villian simply likes other people to suffer, or derives power from it.
Purifier - it is suffering that brings the best out of people; therefore, as tragical it is, they must be made to suffer. Include whatever noble cause it is necessary to do 'minor' evils for, to mobilize the crowd for the right thing.
Holy Mission - actually, it is YOU that are the bad guys - and they won't stop at any noblest or basest deed to eradicate this affront to morality, the only true way of life, their right to XXX, or whatever.
Low time preference - the villain may have a perfectly legitimate goal (become rich, have influence, achieve justice) or not, but doesn't want to wait - or has not the time to achieve it. Hence the "shortcut" and "collateral damage" on the way encountered.
Too much pride - it was a mistake. But a mistake can never be admitted, so measures have to be taken to keep it secret.
Not my rules - a rational being with values and rules that are very incompatible with the interacted society. (A restatement of racial from above, but more general.)
Boredom - what happens if we push this button... or... this man... or... this kingdom? I bet something interesting.