Evil Haka would basically be DC's Vandal Savage, but that character changes quite a bit over his eternal lifespan. To make Haka different from Iron Legacy, one might use a Haka from the far future–either one finally driven mad with loneliness in the Final Wasteland future, or one from a different timeline that ended badly. That could give him not just physical strength, but technology as well. Shock Taiaiha and Atomic Mere?
Evil Absolute Zero would be basically Mr. Freeze. Mechanically that might be too similar to Spite, with his constant HP yo-yoing and bringing out modules instead of drugs.
Of course, Tachyon, Bunker, and Wraith have evil twins in the game already (and DC has the Reverse Flash), although Wraith shows a much darker side in the Iron Legacy future. Wraith might actually make an interesting promo variant of The Chairman, who gets down and dirty directly (though stealthily) herself.
Sounds like we might be getting an evil Visionary and an even-more-evil Harpy/Matriarch as Scions of Oblivaeon. So we can wait and see how (and if) that works out. I've suspected we might get the evil Virtuoso of the Void as a Scion as well, but if we don't, that could be really interesting as well. I'd like to see a mechanic where he attaches melodies, harmonies and rhythms to each other to create composite ongoings with unique effects.
Nightmist might lend herself directly to an Iron Legacy-type "twisted cards" design, and could be legitimately terrifying. She has plenty of reason to be evil without digging at all.
I'd like to see an evil Setback, actually. His cards would have to be changed so that they always have an effect, but that effect depends on the size of his unlucky pool and how many points get expended from it. Easy enough to have an alternate timeline where the drugs that made him twisted his mind like all the other subjects of the Spite program.
As for the Naturalist, I'm thinking of a version that did not repent at the end of his series of transformations. As a result, he transforms constantly and uncontrollably. On his front side, he can have only one form out at a time, like the basic Naturalist, and his one-shots have different effects based on which one is in play. But on his flip side, he can have multiple forms out, representing bizarre hybrid creatures as he becomes more unstable in his rage, which makes his one-shots two or more times as dangerous.