Ok, this is just how I think it could be done myself:
One night, Batman stumbles across what appears to be a giant puzzle of some sort, but is actually a trap. Barely escaping the deadly trap, and assuming that the Joker has found a way out of Arkham Asylum, Batman seeks out Gordon. Gordon, however informs Batman that Joker died shortly after being put into Arkham. Confused, they finally agree that it must be a copycat criminal.
As Batman hunts for the copycat criminal (whom he learns is calling themselves "The Riddler") who seems to be playing a game of cat and mouse, he must also deal with issues at Wayne Enterprises.
There's a new board member at Wayne Enterprises by the name of Oswald Cobblepot. A genial and charismatic man, Cobblepot quickly wins over man of the other board members, and he uses this to get them to do the things that he wants with the company. Bruce is immediately suspicious of Cobblepot.
Eventually Batman finds The Riddler and discovers the he is a man named Edward Nygma. Appearing as little more than an ordinary business man, Nygma wants to finish what the Joker began. He sees the late Joker as the personification of chaos and feels that without the chaos, complete order would threaten to take over and force the city to become stagnate. The Riddler actually believes he might be doing some good.
Around the same time, Bruce has become very suspicious about Cobblepot (borderline paranoid) and does some investigating. He discovers that Cobblepot is a money launderer and a crook, who has ties to the mob.
Just a couple of ideas that I think would imbue the essence of the characters, while also making them realistic and accessible to audiences.
