The Clock King would be an excellent villain for a film, but highly unlikely I think. He's fairly obscure as far as the gallery is concerned, back there but in front of Calendar Man. Cat Man is way back there somewhere. Maybe we need to be ready for Hugo Strange! Get serious man.
Of all the options you've laid before this collective, I think that what we can PROBABLY expect is the appearance of perhaps RUPERT THORNE http://en.wikipedia.org/wiki/Rupert_Thorne
, and the inclusion of Deadshot or, as suggested, an 'original villain'. Somebody's gotta hire Floyd. He doesn't work for free, people. With how the films have closed off so many avenues, Thorne jumps to mind as an old stand by and convenient for plot reasons. Someone will consolidate after Joker and Two-Face tore things up and an old head, as it were, is a sensible choice. Naturally, the boss never takes on the Bat directly so somebody else has to step to the plate, and after using Deadshot in Gotham Knights the licensing issues and 'who has who' shit that DC normally doesn't have too much trouble with are fairly moot. Thorne's whole 'elect me Mayor and outlaw Batman' thing would also fit neatly into a third installment.
Black Mask would be neat but you're just entertaining your fancy man. Get back in the dugout with Link's Loony List.
My money's on Thorne/Hitman X (Deadshot?), Clayface or Mad Hatter being the antagonist(s) in the next film, in that order of likeliness.
EDIT: Also, we are more likely to be the villains in this next movie than Harley Quinne is.