Word has it that Warner Home Video is so happy with the early success of Superman/Batman: Public Enemies that they are considering Superman/Batman 2, the first sequel in the line of direct-to-DVD movies!
If they were to follow the comics, the next storyline in Superman/Batman is the The Girl From Krypton in which Supergirl returns to the DC Universe. The story also stars Wonder Woman as the trio travel to Apokalips to save Supergirl from the evil Darkseid! Does that sound like something you want animated? I know it does to me!
Of course, this is all speculation at this point, but I'll let you know as soon as anything is finalized!