I see it both ways, If they want the Joker in it played by someone else, I'd support it [And I agree with most that it should be James Franco], but if they decided to rest the character with maybe nothing more than a cameo, then I'd be fine with that too.
If they don't go with Joker, than there will probably be a Joker-Esq villain, like Mad Hatter or Harley Quinn, but in a small role, and probably Riddler taking the spotlight as the main villain. As much as I would love to see Johny Depp's version of the character, I believe, as they have done so with most characters, they will cast someone we WOULDN'T expect. Maybe a big name, but not someone who would crack our top 5 "Wish List". They could get freakin' Elijah Wood to be The Riddler, and no one would support it, and then unexpectedly he kicks ass in the role. Who knows?
Interestingly, the new animated Arkham movie looks like it will bridge The Dark Knight and B3, and it features both the Joker and Dent. I think the end to that movie will make it a little clearer as to where they are going with villains for B3.