I really doubt they'll use Penguin and Catwoman in the same movie again.
It depends; doesn't really have to matter if they're both in the same movie. I mean, in Batman Begins, they were able to pull off 3 villians, including a minor cameo of Zsas. It all just depends how you put the story together and who plays their role; I mean, if it were me, I would have Catwoman being one of the more important secondary characters to the story, and Oswald being just there. Maybe just along the lines of importance, so Penguin being as important as, if on a scale, somewhere in between Carmine Falcone in BB and Scarecrow in TDK.
But anyway, to compete with TDK to be an even better film and go along with the fluidity of it's prior achievement, I would say go with Selina Kyle/Catwoman not as a villain, but a neutral character in the story; perhaps either helping or being in the way, like she always is. LOL And as for the main villain, perhaps Riddler or Black Mask. Would love to see Gotham eating itself to shreds as the Joker said, with more theatrical crimes on the street, and seeing this high ranked morbid war between the normal guys (Falcone, Maroni, Cobblepot, ect.) and the freaks, such as Black Mask, the Joker (if possible; doubt it), Two-Face (sorry, but he has a thing for looking dead in the comics and coming back), Bane, Killer Croc, Zsas, and so on and so forth. Meanwhile Riddler slowly rises and sort of orchestrates them together, as he did in Hush.