Nolan did not limit himself whatsoever.
Were he making a massive long line of Batman films or a tv series, I could agree but that is not the case. Nolan saying that he won't utilize characters like Freeze or Robin is not a problem whatsoever because Nolan's world is finite. You can only cover so much within three films. And as long as he has enough material to cover within his three films, he is not limited.
I somewhat disagree. Nolan has largely used much of his films to cinematically explain that his movies are grounded in reality. He made this choice before it was ever decided how many films he would do. Batman Begins is a perfect film. The inclusion of Lucius Fox was a genius stroke, but he still could have found ways to bring villains like Penguin or Croc to the Nolan universe. If he had decided to do a "comic book" world where the fantastic elements were possible, he could have had the same level of seriousness and the same levels of courtroom style drama without the hyper-realism because he could have made his film grounded and less over the top the way the first series of films was.