My thoughts on a few of the 'plot holes',
The leg brace- I actually chuckled when I saw him kick out the corner of that brick wall. Anyone ever lived in an area with brick work still around from ~150 years earlier that has been exposed to nearly constant ~100% humidity? I would wager a shocking number of the people that have posted in this very thread would have very little trouble doing it, they have the structural integrity of thick mud. All it showed me was that he had movement back in his leg, it wasn't a bionic aid in the sense it seems people were thinking.
Raz's appearance- the greatest detective mind in the world is stuck for months in a place with people that know most of the story behind Bane and Talia. We could have a stream of lines from different conversations over the course of months where Bruce pieced it all together, or we could throw out a scene with Liam Neeson and pay fan service and get a quick summation of what he uncovered over the course of months. You could argue that he didn't piece it all together until he had a dream where Raz came to him.
The bomb- a man smart enough to take down the mob, create a fission reactor, build a code base for an aircraft in a matter of weeks using flight mechanics unique in aviation, wouldn't have the sense to have the aircraft drop the fvcking bomb when it got a few miles out? Really? Assuming that it didn't happen to me is a much larger plot hole- Bruce Wayne all of the sudden became a complete retard over the course of sixty seconds. Seriously, how many people in this thread wouldn't be thinking about getting the bomb under water ASAP when they were at a reasonable distance? One of the smartest men alive wouldn't think of it though? Really? I saw it on extra large format IMax, I have 20/10 vision, you couldn't make out the bomb before it went off.
No spec ops teams, no snipers taking Bane down- I honestly thought they spent far *too much* time explaining that Bane didn't have the detonator on him. Several people thought that he was a liar, but it turns out he wasn't. Talia had the detonator on her. He explained it clearly, and it was discussed repeatedly, why nobody was taking Bane down.
Wayne's hookup- Are we going to ignore that as the series stood prior to that scene, Batman was going to die a virgin? Is that really remotely plausible? An attractive orphaned billionaire? Just.... no.
Up until his final conversation with Alfred, he thought that Rachel was going to wait for him and felt honor bound to do the same for her. After that discussion with Alfred, he learned that he had been holding on to a lie the entire time. Obviously her motives were fairly clear on why she wanted to do it, if I was Bruce in that situation I might have been trying to get into Alfred's pants(obviously Catwoman would have been almost anyone's first choice, but she didn't happen to pop up on his doorstep looking to get some).
Batman getting back into the city- Really? The man who vanishes on people in the middle of a conversation on a regular basis, the most skilled ninja the League of Shadows ever turned out couldn't sneak into a giant metropolis? If he had so much as a hint of difficulty it would have been laughable and absurd.
Those are the only points brought up that I can think off of the top of my head. I remember reading through them all and thinking that they were all either explicitly explained or would have been much *larger* plot holes if they went the other way with them.
Edit- Thought of another one, Bane's mask- Raz made it for him, Talia explained it. A man so thoroughly trained in human anatomy would likely know how to create a fixed device that could remove pain from a given part of the body(not using modern science necessarily, perhaps acupuncture - ish).