I personally want the Riddler. Not only has it been set up with the nod to "Mister Reese," but I just think it makes the most sense thematically if, as Nolan has stated, he intends this to be a standalone trilogy.
Ra's in the first is Batman/Bruce's mentor, who helps Bruce to form his code. Basically he "creates" Batman.
The Joker is like Batman's rival. Equal in drive, intent, and creativity, he causes Batman to question his code, but forces him to take on the villain role by the end. In essence, although the Joker causes Bruce to strengthen his own resolve, he weakens his stance.
The Riddler, should Mister Reese become him, would be able to "defeat" the now weakened Batman with the revelation of his identity. With superior intelligence to match Bruce's bucks, there's no telling what he could do. Can you imagine him releasing all (Or some) of Arkum's population AFTER revealing Batman to be Bruce. It would heighten the chase that we saw encapsulated by the end of TDK. Then, by defeating him, he will have overcome three forms of challenge: Emotional, Personal, and Intellectual. It just feels right to me, making Batman a more complex character with each villain.
Also, it takes the villain role from one who sought to do good by creating mayhem (Ra's), one with no intentions other than to cause mayhem (Joker), to one that causes mayhem for his own self-serving purposes.
That's just my rationale though...
Well, that and I really want to see how the Nolanverse would interpret the Riddler's attire.
-Nick