I’ve been thinking about this for some time now. Who will be the villains in the third Christopher Nolan Batman?
Harley Quinn The one villain that came to mind was Harley Quinn. Because the passing of Heath Ledger and the difficulty of recasting The Joker, Harley Quinn would be most appropriate in somewhat continuing The Joker story line. However, she wouldn’t be the main villain in the third Batman.

In this third installment the villain(s) will most likely be Poison Ivy and Bane or Penguin. The Riddler is an unlikely candidate because of the nature of Christopher Nolan’s dark films, and the only person who could really play the Riddler would be Jim Carrey again.

PenguinPenguin is a very dark and vicious figure which would go quite well with Christopher Nolan’s genre of Batmans. Penguin’s creepy love for birds and umbrellas could really mesh in with the current Batman story line.

Poison Ivy and Bane could be possible, but a little less likely because of their origins. Both Poison Ivy and Bane were infused with chemicals and such from plants, which would not really coincide with Christopher Nolan’s more realistic, less supernatural Batman.

So, in my opinion, the two villains in the third Batman should be Harley Quinn and The Penguin. But there has been rumor of The Riddler in the third Batman and an article can be found at The Coventry Telegraph