I read that the other day and had some ideas to address some of those issues:
When and how did Bane find out about Batman’s identity and Applied Sciences? -
When Bane and Batman first meet, Bane knows his true identity. He likely learned this from Talia Al Ghul, his boss, who likely learned it from Ra’s Al Ghul, her father. But the timeline doesn’t quite fit. Talia Al Ghul and Bane were trained when Taila was young and escaped the pit. Maybe around 12. She and Bruce seem to be around the same age so, that was about 15 years before Bruce met R’as in his late 20s. Bruce then kills Ra’s mere months later at which point Ra’s finds out Bruce is Batman. So did Ra’s call his daughter at some point in this small window, tell her Bruce is Batman, then give her the idea to become a Wayne Enterprise Board Member (even though the nuclear device didn’t exist yet) as a long con back up if his plan in Batman Begins failed? Seems like there should be a more concrete explanation as this information is crucial.
And even if that’s how it went down, it doesn’t explain how she or Bane knew about the existence of the Applied Sciences wing of Wayne Enterprises, that it was Batman’s armory and its specific location in the building. Yet they do because Bane was building his hideout right below it. Even if the aforementioned identity leak was possible, Lucius Fox himself said Applied Sciences was “completely off the books.”
John Daggett:
Daggett is initially a trusted member of the Wayne Enterprises board who runs a WE subsidiary construction company. After the events of
Batman Begins damage the lower levels of Wayne Tower, Lucius Fox needs someone on the inside of Wayne Enterprises who can be trusted to discreetly construct a new Applied Sciences Vault in the new Wayne Enterprises Tower across the street, so he gives Daggett's construction company the task.
Fox also needs Daggett to build:
- A secret elevator from Fox's top floor office to the new Applied Sciences Vault.
- A new concrete Bat bunker at the Gotham docks with pop-up equipment vaults and a concealed elevator big enough to lift the Tumbler up to the surface.
- A "panic room" with Batman's equipment in Bruce Wayne's new penthouse apartment and a secret elevator to the sub-basement so he can sneak out.
- The renovations to Wayne Manor and the new upgrades to the Bat Cave.
So Daggett knows all of Bruce's and Fox's secrets but is willing to keep them to himself in exchange for more power at Wayne Enterprises and ownership of the construction company outright. Lucius agrees.
This partnership remains intact until years later when Bruce has retired Batman and is barely a shell of his former self at Wayne Enterprises. He invests most of the company's money in developing a new fusion reactor, which he hides in his old floodable Bat bunker (notice the bunker is nearly identical to the Bat Bunker in
TDK and also is accessed from a secret elevator in the docks next to the river. It would be floodable originally to prevent unauthorized access to Batman's weapons, vehicles, and identity). Then suddenly, after learning that the fusion reactor can be converted into a bomb, Bruce shelves the project and leaves Wayne Enterprises in dire straights financially.
Daggett is furious by this development, so he puts into motion a plan to take over Wayne Enterprises completely and reclaim its former glory. He uses
his brother's (yes, I know they just changed the name for the movie) contacts with the Gotham underworld to set up a plan to bankrupt Bruce Wayne and take over the company so he can restart the fusion project. This gets the attention of agents of the League of Shadows who have penetrated Gotham's criminal element again in hopes of continuing their mission to destroy Gotham. This is when Miranda Tate/Talia al Ghul and Bane learn who Bruce is, how they can destroy Gotham with the fusion bomb, and get revenge on Ras's killer all in one sweeping plan. Miranda infiltrates Wayne Enterprises as a board member to be one of the people who can authorize activation of the bomb.
They use Daggett's construction company to dig beneath the Applied Sciences Vault and Gotham Stadium, and to rig the sewers, bridges, and tunnels with explosives in order to turn Gotham into No Man's Land. Daggett only thinks they're digging into the Applied Sciences Vault, but his second in command is working with Bane and keeping their other activities secret. Eventually, after they are no longer needed, Bane kills Daggett and has the second in command sentenced to exile at "judge" Crane's court.
Blake Intuits That Bruce Wayne is Batman -
WTF, dude? First of all, I’m highly skeptical that anyone could “see” just by looking at Bruce Wayne’s face that he was Batman. But even if this were not-at-all implausible, the fact that this development occurs in the first act of the film is a strong indicator of this film’s issues (namely, the need to cram in as much plot development as possible). In any other film, such a reveal would normally come after the end of some sort of prolonged interaction between these two characters, where it might be somewhat understandable that one character saw the truth in the other. Here, they get it out of the way right from the beginning in a fashion so abrupt that it has no emotional resonance whatsoever.
Also, if Blake was able to put this together, wouldn’t other Gothamites have started to put two and two together? As a separate issue, by the end of the film, practically all the main characters already know that Bruce Wayne is Batman. By the time Commissioner Gordon figures it out while Batman is taking off, I didn’t think “Wow, what a revelatory moment!” Rather, I thought, “Oh man, he is so late to the party on this one.”
Remember when Batman saves that little bastard Joffrey from
Game of Thrones during the fear toxin rioting in the Narrows during
Batman Begins?

(Ned Stark says thanks, Bats)
I'm making that kid post-Crisis
Jason Todd. His parents were living in a slum in the Narrows and constantly fighting. Batman gives the kid a pair of his night vision goggles and later after saving them during the riots Rachel calls Batman "Bruce" right in front of him.
So, the kid's dad gets sent to prison, and his mom ODs, which means he gets sent to St. Swithen's Home for Boys where the older John (Robin) Blake also lives. When the kids exchange stories about Batman, the blond kid mentions that he has his night vision goggles, that he met Batman, and that his name is Bruce. Later when Blake first meets Bruce Wayne, he uses his deductive skills (along with seeing the haunted look on his face) to determine that this is the Bruce the kid was referring to and that he is Batman. He simply omitted mentioning the rest of it to Bruce and went for the more personal connection between them.
After
TDKR when John/Robin Blake starts to become the new Batman, he could contact Jason Todd and have him become Robin, and perhaps even contact the now adult Barbara Gordon to become Batgirl and eventually Oracle after Joker shoots and paralyzes her after escaping BlackGate Prison during
TDKR. Blake will need a team to support him as he initially lacks the training, skills, and resources of Bruce Wayne.
Why Wouldn’t the SEC Just Overturn Bane’s Fraudulent Trades -
I mean, it’s pretty clear that they were done fraudulently, right? Else what the hell did they think Bane was doing there?
They will, eventually. Fox just said it will take some time to sort everything out.
Also, the League of Shadows has used financial means to topple governments before, and has infiltrated the highest levels of governments, so is it not possible that they have people at the SEC who might make things difficult? It would sure explain the too little, too late reaction by the SEC to the short selling and credit default swaps during the credit crunch in 2008 and the subsequent Great Recession. It was the League trying to destroy the world economy.
Christian Bale and Marion Cotillard Have Sex –
On the one hand, yes these are two very attractive individuals. Why shouldn’t they give in to their carnal desires? On the other, more reasonable hand, there is virtually no development in the relationship between these two. They’re running in the rain, then they start making out, then in the next scene they’re naked. If only real-life romance worked like this…
Seriously though, with no emotional attachment to this relationship, Talia’s eventual betrayal is nothing more than a Shyamalan-style twist with no impact behind it. A missed opportunity.
I don't get the complaint here, frankly. Bruce was just destroyed financially, outsmarted by Selina, is physically and mentally in pain, and lost the only friend/mentor/father figure he had in Alfred. Is it not understandable that when he's at his lowest point that he would turn to someone who offered companionship, and who --bonus-- happens to look like Marion Cotillard? You don't need the Riddler to figure this one out.
Plus, did people think Bruce never did anything with all those women he was wining and dining while he was putting on his playboy persona in better days? Sure, he was pining for Rachel too, but I think news would get around town if Gotham's wealthiest bachelor always dropped the women he was dating off at home without sleeping with any of them. He seemed to have some sort of ongoing relationship with the ballerina in
TDK. So, it's not like Bruce was a priest or anything.
So Batman is a street artist now? -
After months away, being mentally tortured and physically broken, Bruce Wayne returns to Gotham. He spends the first few hours of what could be the final day in Gotham history getting purposely caught by Bane’s cronies, a huge risk, and then escapes and saves Commissioner Gordon and John Blake with mere seconds to spare. Yet somehow, with this impossibly frightening ticking clock, he finds the time to use gasoline to make a huge Bat symbol on the top of a bridge with the knowledge Gordon will be there, pick up the flare, and light it up. Theatrically is part of Batman’s persona, yes, but it seems like there might have been a better use of his time.
He didn't know Gordon would be there when he initially set up the display, but he knew that was where Bane and the criminal element of Gotham was exiling/executing the wealthy and enemies of the movement, so it was a logical spot to get their attention.
How Does Bruce Wayne Get Back to Gotham? –
How does Bruce Wayne travel back to Gotham in a matter of days with absolutely no resources what-so-ever? No only is he bankrupt, but Alfred has disappeared, he has no identification of any kind which includes the necessary passports to get back into the United States. Even if he somehow gets through customs with no delay, all the entrances to Gotham City are being guarded by Bane’s thugs. The Bat is stuck on a roof of the building where Wayne left it, so he doesn’t have access to his new flying machine. And speaking of which, somehow The Bat has not been discovered in the months Wayne has been exiled in the prison. Are we supposed to believe that no one checked up there during Bane’s occupation? Or maybe that the sheet of camouflage has kept the secrecy? And when Bruce Wayne gets back, how does he know exactly how much time is left on the bomb and where Selina Kyle will be?
First off, he's the goddamn Batman. That's really all you need to know to explain those things. However...
Did they miss the entire first third of
Begins where young Bruce drops all of his money and possessions on the spot, hops on a ship heading overseas, and travels the world for the better part of a decade without a dime to his name to learn how the homeless, starving, and the criminal element lives? He knows how to get anywhere in the world without any resources, and how to sneak back into the US on a ship.
In each one of the movies Bruce winds up in Asia either in prison or doing something illegal (in China and India respectively). It's logical to assume he might have some resources staged throughout Asia just in case he needs to make a quick getaway. Hell, the same guys who did the
Fulton STARS blimp and hook kidnapping of Lau in Hong Kong were nice enough to lend their white C-130 to Bane to snatch the CIA plane, so clearly they're still in business. Maybe Bruce used his prior relationship with them to bum a ride back to Gotham with the promise of future payment and then parachuted into the city.
Or, Bruce hitched a ride on one of the many food, water, and medical supplies shipments coming into the city to sneak back inside, just like the special forces team did.
As far as where the Bat was hiding, I assume it's atop the building where his penthouse apartment is (the one that must have a secret elevator for him to sneak in and out on), so no one would likely mess with it, at least until someone else bought the apartment, but that wasn't happening during No Man's Land.