Could there be a sequel? Well that's what the Mania and MTV Splash are reporting...

Apparently sales for Superman/Batman: Public Enemies have been good, so a possible follow up might be on the cards. Both Mania and MTV Splash have speculated that the "The Supergirl From Krypton" would probably work best as the sequel to “Public Enemies”, since it directly followed “Public Enemies” in the original “Superman/Batman” comic and set up the subsequent storylines.

Personally I think the story where Superman and Batman have to hunt down all the Krytonite on Earth to make it safer for Superman was one of my all time favorite stories. Next up will Justice League: Crisis on Two Earths so who only knows what will be next on the animated scene for DC?

(Source - MTV Splash / Mania)