...the focus was taken off villains and Batman was again made the focus of the story?
...the focus was taken off villains and Batman was again made the focus of the story?
Nope. You always run a risk with making another installment, and to run away just because of success is uncharacteristically spineless of Nolan and co. Besides, their story is not finished. We know they pitched 3 films, and we know that TDK's ending paves for a new arc that HAS to be finished.
Godfather was more of a bookend than TDK was, and THAT got a sequel. A very great one I might add.
Batman didn't get pushed to the side by the villains in TDK.
"The better the villain, the better the film". Alfred Hitchcock.