I was thinking about this the other night, and I just remembered it... What if The Riddler had his own new mob, only this time, a mob of "freaks," so to speak.
The best comparison I could think of is Charles Manson.
For Batman 3 to be as heart-pounding as TDK was (and for The Riddler to be a more dangerous follow-up to The Joker), I think there needs to be more at stake than Bruce's identity. As we know, The Riddler doesn't kill, but I think alluding to a Charles Manson-type situation, it would not only stay true to The Riddler's moral while still twisting him into a much more dangerous, life-threatening adversary. In this case, Bruce's identity is on the line, but so is his city and the lives of its inhabitants. A situation in which one stake would be put against the other would probably create a damned good thriller of a movie.
The Riddler could have his own group of followers that do his bidding, which would leave The Riddler as nothing more than a conspirator with such loving followers that none of them would allow trace back to Edward.
Not only that, but if The Riddler is being manipulated by a higher power, much as he was in Hush's comics (only this time by... Bane, I think would be the best option), I think it would make the story even more twisted and maniacal.