>>15340206He wasn't really an "Evil Leader"
Other leaders knew they were evil, they were set on that.
Lysandre was a man who was quite powerful and important in Kalos. He wanted to help Kalos for the better. But after time, he became disenfranchised with the region. His world views became darker and grim.
He thought he had to do something extreme to save the world he used to love. So he came up with his plan to kill everyone deemed "bad" or what have you.
The thing was, he wasn't some evil mastermind like Ghetsis or Cyrus or Giovanni. It's pretty evident in his henchmen. They're more concerned in fashion and appearance than battling. And his executives and scientists were merely his employees from Lysandre Labs.
If anything, Team Flare was more of a cult led by a man who went down the wrong path than some evil team.