I thought it's been covered that this trope is about more than a villain's ACTIONS on this wiki. Ghetsis might not have done the things Darkrai did, but at the very most he's portrayed as someone with the capacity to do the sort of things the Cipher Leaders or Purple Eyes did were he only to have their resources at his disposal. There's no way a man whose entire motivation is based on self gain and entitlement and who is also a serial torturer and exploiter would not jump at the chance to use that sort of power so long as he benefits. And he's one of the more shamelessly sadistic characters in the franchise too, meaning that the suffering of others would be more than just collateral damage to him, but an added benefit.
Cyrus attempted omnicide, but it was as means to the end of eventually recreating everything he'd destroyed, but devoid of spirit, which he believed would make them better. Lysandre attempted mass homicide, but it was for a cause he believed was justified and his weapon didn't seem like it reached too far beyond the Kalos region. Ghetsis was going to take over the entire world all because he was power hungry and entitled, and since only he and his followers would use Pokemon, they'd control the entire system of said world and use that as means of oppressing and enslaving everyone alive, who'd be legally prohibited from having Pokemon to defend themselves with. Basically, it would be a Dystopia where every day of living would be one of torture if you're not Ghetsis or one of his cronies. That end goal sounds like a Fate Worse Than Death to me.
And Cyrus didn't torture the Lake Pokemon in order to make them comply with acts of terrorism on others - he just wanted to extract their power and make the Red Chain, after which he allowed you to free them. The crimes are the same, but the motives and results differ, with Ghetsis coming out looking worse since he made Kyurem suffer specifically so it's power could then make others suffer.
Seriously, this sudden opposition to Ghetsis on the trope due to lack of "baseline heinous" actions came out of left field. I thought you were better than this. Would you also think Hunter J and Charon in DPA shouldn't count since they didn't do the more heinous things that Cyrus did? Unlike Ghetsis, they're actually featured in the same stories that feature Cyrus!
And who IS the other candidate you have in mind? Ardos? Cyrus? Lysandre?