I'd definitely pick up the villains who were not in Nolan's series yet still maintained at least somewhat a realistic appearance in the game (like Harley Quinn). Otherwise, I'd feel too weird, showing the other-worldly, fantastical characters next to my gritty, realistic figures - and my budget doesn't extend to two separate collections.
But make no mistake - this game DOES look awesome. In 15 years, I haven't seen a game that does Batman justice. Nothing as awesome or true-to-the-source material as he deserves.
But it looks like this situation is soon to be rectified.