I agree to a certain extent. It's true that it's easier to put the focus on Bruce in an origin story, that's first and foremost about how he came to be. But it's not necessarily true that including Joker and Two-Face prevented Nolan to do it again in TDK.
The stakes were as high in Begins as they were in TDK. In both cases, Gotham was facing total destruction. But in one case it was through the use of Scarecrow's fear gas, and in the other it was through the influence of a madman trying to wreak havoc and have people give up on all hope of saving themselves through order and unity.
Now, Scarecrow happens to be my favourite Bat-villain, and if the Joker is the ultimate archnemesis in the bat's gallery of rogues, Ra's al Ghul is certainly the most influent and the most dangerous if you only look at numbers (Joker often threatens the lives of Gothamites, but Ra's very often tries to take over/destroy the whole world).
So in a way (my way) Begins had greater villains. Not fan favourites perhaps -if you compare them to Joker and Two-Face- but great anyway. And yet it managed to keep the focus on Bruce.
I hope TDKR will do the same by having Bruce face a level of threat that's so above everything he's ever faced and hurts him on such a deep personal level, that the movie will end up being about him and what he is, rather than being about "this new threat that has to be stopped".