Bruce's greatest enemy could very well be himself. The events of TDK leave lots of room for guilt trippin (sounds groovy...), and it would actually be pretty interesting to see some self-deprecation themes come into play. Although I'm not sure it's something Nolan would cover, to me, it wouldn't feel totally out of left-field, and I would definitely welcome it. In one way or another, a common trend in Nolan's films is that his protagonists have all been flawed characters that subtly comment on facets of the human condition. It would be neat to have one of these characters self-aware of their flaws, and actually voice their concerns/disappointment with such issues. We haven't really seen Nolan go that route yet (although there are definitely elements of it in his films - Bruce in BB saying that he failed to save Gotham, reflecting on his failures in TDK after Rachel's death, Cobb confronting Mal about her projection not being good enough for him, etc. etc.), and I think Bruce in Rises would be a good opportunity for some more exploration and experimentation. And there are multiple ways to go.
You could have him harp on himself for not being able to save Rachel and Dent and Gotham, but at the same time, you could have Bruce angry with the fact that he feels so much pain and guilt - he despises that he could be so weak. I think an intriguing element to add to Bruce's arc would be that of his "invulnerability," which I discussed with Saint when we were chatting about the aftermath of a beat-down from Bane. Perhaps it would be cool to not only touch upon that in a physical and mental sense, but an emotional one as well. One of Bale's final scenes in The Prestige comes to mind, where Borden is frustrated with himself (
) for not being smarter than Angier. "Why can't you out-think him!?!" Again, that idea of Batman being "invulnerable" leaves a lot of doors open, and paints an interesting canvas for the conclusion of Bruce's arc. Just put yourself in his shoes:
"I'm supposed to be this elemental, terrifying being...this inhuman symbol that will not quit, and yet here I am, physically broken and emotionally compromised. I'm grieving over lost friends, like a man, whereas I embarked upon the path of becoming a legend. And most importantly, I'm stuck questioning whether or not I'm actually capable of being that legend, that 'Batman' that I think I should be. What do I do now?"
Gordon also factors in to the issue of "invulnerability." How exactly does he view Batman, especially now after they've been through so much together? What does he think of this man, who puts so much on the line, night in and night out, and only seems to get crapped on for it? How can such a man take it all without cracking?
I think that type of thought process (I'm referring the part about Bruce's mind above) would definitely be something fresh, and it adds a new level to the usual superhero "brooding." Instead of the hero pondering giving up the cape and cowl, or how hard it is to do what he does, we get a man who wants to devote himself to the ideal, and squirms at the notion that his human emotions and struggles are holding him back. And then of course, Selina, Alfred, Gordon, Lucius, and the "why do we fall?" idea can all come into play. Bruce may think that his humanity is holding him back, but perhaps he learns that it's the only thing left that separates him from someone like Bane, the Joker, etc. It's what makes him so unique. It's that sliver of humanity, that fraction of hope and of faith that remains. This point sheds a little more light on what exactly makes Batman a watchful protector, as opposed to some nut in a costume who happens to not murder (surely this 'murder' part will bring out the vultures and be argued
).
Anyhow, I'm almost 100% certain that's not the type of answer that the OP was looking for in regards to the topic, but the thread name inspired me to write up my thoughts on who, aside from the main villains, Bruce's "enemy" could be.