Nolan spoke to this in an interview for Empire-Online. In short, he simply found it difficult to imagine Robin fitting into the world he'd created:
Q. We have to ask about the Robin gag at the end. We’d always wondered how possible it would be to make that character work in this version of the Batman universe, and this has to have been the only way.
It is a little hard to imagine Robin working in that universe, so the idea had to be limited to that gag at the end. Nolan: It is a little hard to imagine Robin working in that universe, so the idea had to be limited to that gag at the end. But Joe’s character is very important to the story. In any movie you need a character looking at proceedings the way you see them, and Joe’s character is that character for this film. One of my favourite scenes is when John tells Bruce how he knew he was Batman. It’s like that scene in The Prestige where the little kid sees through Christian’s trick. Little kids, they don’t have any illusions, they just see the truth of the situation. I feel there’s a kind of spiritual connection between the two movies there.