Them looking similar hasn't been a big deal before. They even starred together in arguably the best movie of Heath Ledger's career...
That's my little sister's favorite movie. For a chick flick, it's really good.
Going through a list of Batman villains, I don't think there's a lot that will work terribly well. Many of them don't seem like they would fit with the very realistic society Nolan has established.
Harley Quinn would be too shallow without Joker in the movie, Killer Croc and Clayface are unrealistic and cliched, and many of the other possibilities are cheesy or wouldn't fit with the universe.
I think The Riddler is the most obvious possibility as a main villain; he is well known amongst casual Batman fans, doesn't have any extremely strange qualities that would ruin the integrity of the reality of the world. The Penguin is a slight possibility too if done right imo.
I wouldn't mind seeing Zsaz in a minor role.
Besides Riddler, I think Penguin would work pretty well. He's born with a deformity, like in
Batman Returns. (In fact, since it's on topic, I liked Tim Burton's directed/written movies more than the one's he produced that Schumacher directed. Schumacher kinda gayed it up to be honest. Like, Burton's were weird, but they were still more gritty and realistic... Though definitely not on Nolan's level.)
I like the idea of Croc, but no one's ever going to touch the Joker. The Joker is Batman's nemesis. He's his counterpart. As crazy as Batman is, Joker is crazier. as dark as Batman is, Joker is darker. His existence is to be the Satan to Batman's God.
With him completely out of the picture, who do we go with?
Hush could be good, but he's not as easily identified.
Catwoman, Poison Ivy bring in the feminine element. It just has to be done properly. And I have no doubt Nolan could do it.
Your knowledge of Batman's rogues gallery seems limited at best. There's plenty of good fits for the Nolan universe.
Everyone's is limited at best compared to you. Don't be a douche, just throw out some ideas.