I have read them, I actually love them. But on film, I would have feel a little cheated if they said that there were more, ahm, "super criminals" in the interim between TDK and Rises. Because I would have wanted to see them, specially see the Nolan's take on them. Since Nolan desired to end the story, instead of infinitely blowing up the balloon and expanding the story, I found appropiate his creative choices. Those gaps are opportunities, yes. But then, we would need another director, and perhaps his vision would compromise the themes of the trilogy, who knows?
I was the first on the line who have wanted to see the Riddler in the sequel. I wanted him badly. See for example this great fan film:
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As a short tale, it can fit easily in the Nolan Batworld, but really deserves a bigger canvas. But while giving the story the weight it deserves, it would change the ending in a big way.
Having a villian would serve a similar purpose like The Joker in TDK, because that's why there are so many villians on the comics. Not because they are similar, but because probably the feeling would be the same. Just like with the previous films and the comics, and the cartoons, the question would be "Which villian would Batman fight next?". There is nothing wrong with it, in fact I love it. It's a different form of telling a story, but from a storytelling standpoint, as films it would follow the same template. Nolan with the three films explored different themes, and they are quite different and cohesive at the same time.
There is a need for Batman to fight adversaries in a regular basis, because the format demands it. On film, not so much... unless you are willing to go the high road and make a long string of films, which is hard work. Perhaps now we can see a Batman with a vision that allows for a greater world, but in my opinion and experience, it would be hard to find the emotional resonance that Nolan achieved with his films.