I'll preface this by saying up front that a lot of the so-called plot holes people complain about aren't really plot holes upon further examination, and I overall like this movie quite a bit.
That having been said, I still have questions and issues (some of which aren't necessarily plot holes, either):
1. How does Blake really know who Batman is? While Blake's backstory explains why the two would feel a sort of kinship and bond easily, and also why Bruce would see him as a worthy successor, it does nothing to explain how Blake figured out he was Batman. Sure, WE know as the audience to associate being Batman with being an orphan, BUT THE PEOPLE IN THE MOVIE DON'T KNOW THAT CONNECTION! How does he know whether or not Batman is an orphan? HE DOESN'T!
2. Batman coming upon Selina Kyle just as she's surrounded by Bane's mercenaries at Dagget's place. Bruce JUST escaped from the police. Wouldn't he want to lay low from police or press helicopters just after that scrap? And did he even know that Dagget needed to be looked into at that point? I thought he only learned his connection to Bane later on? And even if I have that part wrong, he didn't yet know it was Bane who attacked the stock market; he only saw him with the bike helmet on, hiding his face/mask.
3. When Batman first fights Bane, what happened to the rest of his arsenal? Why not use the grappling gun? Why not use one of his mine/grenades you see him use later when he shows Blake how to use one? If you want to get really nerdy... how about using that device in the heal of his boot to call the bats back in like in Begins? I think even Bane and his crew would have struggled with that long enough for him to get away and regroup, right? I basically just chalk this one up to plot necessity, but it still somewhat bothers me.
4. Are we supposed to believe that in a Gotham city virtually devoid of any police, with at least Blackgate prison being freed immediately, that no other prisons were freed during those months? I mean did they just let them all starve in their cells? Because if not, there's the elephant in the room of the fact that Joker didn't die in TDK and he likely would have been in the middle of all of that anarchy while Bruce was stuck in the pit.
5. As soon as Talia knew Bruce was back in Gotham... why the hell not tell Bane, #1, and then why the hell not go ahead and push the detonator before he has a chance to **** up their plan at the last minute?
6. When the police rush Bane's mercenaries in the streets, why the hell didn't the automatic weapons the mercs had kill at least 4 times as many as the 'whopping' handful of cops that dropped dead? That made no sense.