This season on Gotham had Edward Nygma (Cory Michael Smith) embrace his the Riddler persona and go after his once friend Oswald Cobblepot (Robin Lord Taylor) aka The Penguin. But the newest DC Versus pits the Culprit of Conundrums against the Clown Prince of Crime in a battle of wits and fits. Where Nygma is brilliant, he is also hampered by his obsession over puzzles and riddles which can be used against him. Joker on the other hand is insane, completely insane, and has the ability to figure out what makes his opponents tick and attack where they are most vulnerable.
Since neither of these villains have any real superpowers, it would seem like a fair fight. But Nygma often times defeats himself because of his clues while the Joker is without moral or social norms that would prevent him from doing anything. He has no limits, which means he can go to places that the Riddler can't and happily laugh in the darkness. I think where the Riddler is a formidable foe against any hero, he is limited in going against someone who doesn't think logically, which is exactly the Joker.