What are some possible ties between Hero and Villain?

Some of you may know I’m working on a comic. I’m playing with the idea of my heroines being a superpowered shapeshifter (body-weapon, not person-mimic) and a waitress (her April O’Neill, if you will). They’re generally spunky, down-to-earth, and don’t have much backstory yet.

My villain is a necromancer, and a high-ranking leader in some occult group of magic-type supervillains, similar in personality and looks to the “Fat Man” from the Maltese Falcon.

I know good villain-hero stories usually have a tie between the two (batman and joker, both crazies in suits; lex and superman, both orphans, spider-man and venom, both had the same suit/powers), so that the story is interesting and personal, plus the villain gets a “We’re not so different, you and I” moment.

At this point I’m willing to consider anything. My writer’s block is killing me.