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What everyone here seems to not get is that what counts as "evil" boils down to character. Yes, genocide is about as evil as you can get, but Lysandre felt he had good intentions behind it all. Heck, the man even cries at one point because he has to resort to genocide to "fix the world", and sees no other alternative. Again, his goals and plans may be evil, but the guy himself is not. Like Thanos, all he wanted was a better way of life for everyone, but felt that commiting the most heinous of crimes was the only way to achieve that.
Ghetsis on the other hand is completely evil as a character. He is remorseless in the way he treats his son, and uses his special gift to accomplish his goals. He sets up a very altruistic image that is only a facade for a madman that wants power. Unlike Lysandre, Ghetsis knows what he's doing and knows there's no greater good ideal behind it, it is all for his self gain. When his goals fail, instead of reconciling with his son or congratulates the MC for their strength, his breaks down in anger, insulting and berating everyone around him. He is a high grade sociopath who sees himself as the only one fit to rule and lead, everyone and everything around him is just a tool. The ultimate irony with Ghetsis is how he accurses N of being a "freak without a human heart", yet it is Ghetsis, in his all consuming lust for power and the absolute lack of respect for everyone around him, that makes him the one who lacks a heart.
So to sum up autistic tirade, Lysandre may have the most evil goal in Pokemon, but Ghetsis is the most evil as a character. Lysandre was a bleeding heart who felt the path of destruction was the only recourse left to saving from his POV, a doomed world. Ghetsis was a megalomaniacal sociopath who only wanted power for himself, because he can. He on the other hand would gladly lead the world to ruin if it meant he would sit at the top.
