Secondly, the bounty is EXTREMELY exaggerated, and Batman isn't that intimidating yet; he's been in the game for just two years, and most thugs don't even believe he exists, plus Gotham is still pretty much in Black Mask's pocket. Black Mask wouldn't waste that much money when he's still on top of the game.
There's also the ludicrous amount of explosives under the bank, too much to just rob a bank. And why would Black Mask even rob a bank by himself, or at all? But remember the trailers: Joker set up explosives across various buildings, just to mess with Batman.
Black Mask wouldn't kill Loeb, but Joker only cares about spreading chaos. He wants to kill Batman out of Roaring Rampage of Revenge, and only Joker would be crazy to throw in 50 million dollars to cause mayhem through Gotham.
This game also explains some of Joker's alliances in Arkham Asylum and Arkham City. Why he's so friendly to Killer Croc? Because Croc worked for him before (It's unclear if he knew Joker had traded places with Black Mask, though).
Given that one of Croc's natural abilities is enhanced smell, it wouldn't be a huge jump to assume that he did know. That raises a different point of Fridge Horror, though: if he can tell Batman is behind him just by scent, it stands to reason that he might be able to guess his identity if he ever meets Bruce Wayne in person.
I recall a comic where Catwoman mentions that Batman uses some kind of ointment to protect his exposed jaw, which could presumably also mask his scent. He thinks of everything, remember?
He considered offing Calendar Man just because it was Christmas Eve. That really sounds like something The Joker would find funny.
The game marketing campaign made extensive use of the phrase "Your enemies will define you". After playing the game it is pretty obvious it was not only about Batman. Bane and specially the Joker were defined by the events of that Christmas night.
Penguin claims that all arms deals taking place aboard the Final Offer are completely legal, due to the vessel technically being property of the Somali government, and thus a small bastion of lawless foreign territory; while he is correct on that count, the police are still able to go after any of his customers for smuggling weapons into the United States. Not that he cares.
Batman finds Bane's hideout by following a tracker he planted on him back at the hotel. Bane's Venom delivery system was damaged there as well. Bane found the tracker when he repaired his delivery system.
Something that people have complained about is how the combat is less forgiving than the previous games—thugs are faster, counters require quicker timing, etc. But it makes sense for them to be like this in this game, which takes place in Batman's second year, and is about 5-7 years before Asylum. That's about 7-9 years of fighting Batman, who won't hesitate to snap their bones, beat them into submission, use specialized weapons, or use the environment against them. The thugs in Gotham City are a clear, yet still effective, case of Dented Iron by the time Asylum happens.
Also, Batman has probably just become more experienced over those years, making countering the mooks a more trivial matter, due to being able to read their moves more efficiently. This could also explain their apparently lower speed: we're playing as The Bat, and they seem slower to him, for the same reason: regular mooks have become even more routine by then.
There are way less mooks around in the chronically later games in the series, of course - since Batman proved capable of beating the hell of them all in Origins, a lot of them probably just packed it in. Not mention the newly risen super villains dominating the Gotham underground would have started killing them off from time to time. This also explains why the mooks in Asylum and City aren't as tough, too - they're either comparatively newbies or suffering a few years worth of bad road.
Critics question why Batman is more prepared or has the same/better gadgets as in other games. Well:
Batman can fly back to Batcave, something he couldn't do in the earlier games.
The plot of Arkham Asylum has Batman underprepared and forced to improvise the entire game with his gadgets because he is caught off guard by Joker.
In Arkham City, Bruce is thrown into the mega prison without any of his gear, and has to have it all flown in, even making extra requests when the situation called for it.
Batman created the glue grenade, which is functionally identical to the Freeze Grenade, but keep in mind that the Freeze Grenade wasn't his invention, Mr. Freeze gives it to him to help him take down the Joker. And in "Cold, Cold Heart" it is revealed that the Glue Grenade was unstable and didn't last longer than that one night.
The Accelerator actually is not as good as the Grapnel Boost. The Boost is probably an upgrade of the Accelerator.
The Accelerator was designed to work with the Origins suit, which is much more bulky and more like Powered Armor. The force of it is against the suit rather than Batman's arm. The Boost was designed to work with the much lighter high tech fabric suits Batman had switched to (for more mobility and less noise), where the force of it would be against Batman's arm. Different tech. Notice he switched back to an Accelerator type thing (but more more powerful) when he switched to the super armored suit in Arkham Knight.
The remote grapple is similar to the line launcher but not as effective because it can't hook to any surface like the line launcher.
So it isn't so much of whether or not this equipment still exists during Asylum and City, it's a matter of whether or not Batman felt like he actually needed to take it with him. Just like how he switches from heavy metal armor to the sleeker, slimmer suit. (Real Life development choices notwithstanding.)
People claim that Harley's interview with the Joker retcons what had been established in Batman: Arkham Asylum, but thinking about it, it helps make sense of some of the oddities:
Why would Arkham's staff let a an inexperienced intern provide therapy for the inmates? Harley wasn't completely inexperienced at the time, having worked for Hugo Strange's clinic and Blackgate Prison (which justified her interviewing the patients), but she was still hopelessly naive, which the Joker took advantage of.
Why would they let anyone interview the Joker, given what he tends to do? He was still new to Gotham, so nobody knew what he was capable of, and since Harley appears to be transferred to Arkham in the final cutscene, she might have been among the first to interview him.
The interview at Blackgate was off the record, and somewhat informal. The interview at Arkham Asylum was later, on the record, and therefore official and recorded. It doesn't matter that she had interviewed him before at Blackgate, procedures are procedures. This type of red tape is very common in both law enforcement and mental health facilities in real life, so it makes sense.
The fact that Deathstroke is playable in Challenge Maps seems odd, given that previous characters have either been Batman's allies (Catwoman, Robin and Nightwing in Arkham City) or the Joker in a (somewhat canonical) prequel to the events of Batman: Arkham Asylum. However, given that the Challenge Maps in this game are a simulation (being accessed from a computer in the Batcave), we can see the Deathstroke maps as a way for Batman to study him in preparation for a fight (since he knows Deathstroke is after him, but not when he'll attack). It also neatly explains how Batman is able to counter everything Deathstroke throws at him - he's already prepared.
In addition, since Deathstroke is one of the foremost martial artists in the DCU, it's not hard to imagine Batman studying his style even after defeating him, to see if he can find any new moves to adapt and fit into his own style.
This could also explain why Deathstroke and Tim have similar movesets; As Jason was killed after getting the same Robin training as Dick did, why shouldn't Batman try to teach the next Robin a different fighting style. And Batman just happens to have a simulation of the world's deadliest assassin.
During "Cold, Cold Heart", when Penguin declares that he's going to freeze to death and Batman says that's not his problem, it was initially a bit confusing considering his general stance on saving the lives of the people he fights. It is possible to explain it with him thinking he would have enough to time to go back and save him after the ordeal with Freeze. There's another explanation though; Penguin was frozen with Victor's brand of cryogenic weaponry, which Batman states puts its victims into cryostasis. Even if Batman doesn't save him, he's not going to die.
Joker's Multiple-Choice Past has a constant, as Strange pointed out: Batman was always responsible in some way. Then Origins came out, and it's revealed that Joker found his purpose in life: fighting Batman. That was when Joker was really "born".
In Batman: Arkham City Firefly, one of the world's greatest assassins, isn't present despite the game saying that all of Gotham's criminals are imprisoned in Arkham City. Like the Joker entry above, Origins provides some answers: he's either used his contacts to flee the country after the escaping from prison, in Batman: Arkham Asylum there's a newspaper stating as such in the medical center, or he's been recruited into the Suicide Squad.
In this game, it's revealed that there's a hidden drug lab in the east part of the Steel Mill. In City that whole section is on fire. Until this game, one would think that it caught fire because of the dilapidated furnace, but it's also possible that Joker first used this place to create a cure, only to torch it out of frustration. It certainly explains why Joker would let Freeze use the old police lab.
Late in the game, Killer Croc just up and leaves after he gets hit in the neck by a stray bullet, even though he got caught in three explosions just a few hours earlier just fine. Fast forward to Asylum where the his shock collar is around his neck, and it's strongly implied that Croc's neck is a weak spot. It may also jump to Fridge Horror; Croc may have tried to hang himself to escape the torment he received due to his appearance.
People have complained how Batman can get punched through a concrete wall by a TN-1 infused Bane and get back up. By let's remember that the bat-suit allows Batman to drop from high altitudes and land without a parachute, perfectly safe. When he was getting punched, the force was enough to trigger the shock absorbers in the suit, mitigating the actual damage Batman took.
Here's a double header for the Lacey Towers case:
Dr. Young basically lives next door to Black Mask's safe-house. Given that the Enigma data located there would have been planted after the murders, it wasn't damaged by the fire or Joker just for kicks, someone busted into the safe-house after the murders. Since Young's door was taped off, she was the one who called the cops over after investigating the noise, and was moved by the cops for questioning.
Whoever planted the Enigma data must've been from Penguin's gang because how else would Penguin know about the murders.
In Cold, Cold, Heart the Remote Claw lost its zip-line function. In Origins Blackgate the Line Launcher has gone from a prototype to a mass-produced gadget. Batman removed the zip-line to perfect the Line Launcher prototype.
A small but very neat detail in Cold, Cold Heart, throughout the DLC, Batman is on a First-Name Basis with his apparent friend, Ferris Boyle, and refers to Victor Fries exclusively by his supervillain moniker, Mister Freeze. Upon finding out exactly what happened to Victor, what he wants, and the sort of man Boyle actually is, Batman immediately switches to First-Name Basis with Victor and Last-Name Basis with Boyle, showing exactly how far his opinion of the Corrupt Corporate Executive has fallen.
A few regarding the Bat-Mobile:
It's undergoing maintenance during the game because the storm has blocked off the city roadways, so there's no point in having it ready.
The Bat-Cave seems to be designed with just the Bat-Wing in mind, since there's no bridge in the cave for the Bat-Mobile to exit out of. It's likely the Bat-Wing was Bruce's primary vehicle at that time, and the Bat-Mobile was stored in an area of the Bat-Cave that we don't have access to during the game.
Wherever the Bat-Mobile is stored, it must be somewhere that can lead to the wine cellar, otherwise Bane wouldn't have gone through the tunnel as mentioned in Cold, Cold, Heart.
If this is all true, than it's possible that the Bat-Mobile was also meant as an escape device for Alfred.
In 2015, it was revealed on a cryptic YouTube channel that there was an undiscovered Easter Egg in Batman: Arkham City where Calendar Man tells Batman he was there at the beginning and will be there at the end. Surely enough, at the beginning of Arkham Origins, Calendar Man is present. And at the end of Arkham Knight too.
Listen closely when Bane shouts in his last boss battle. It's a distorted scream of "WAYNE!". Even as a rabid animal, he still remembered that Batman is Wayne until he was electrocuted into unconsciousness. What if Bane had been just a little more resistant to TN-1 and started shouting "WAYNE!" intelligibly?
After Batman finds his hideout, he sets off an explosion to destroy Bane's computer. We don't see Batman planting an explosive, so he must've detonated the tracker. If Batman was willing to kill, Bane would never have left New Gotham, let alone reached his hideout.
Bane's gang isn't around in the other games. Did they all give up on Bane and leave, get captured, or killed in the interim?
The game implies that Calendar Man is busy killing a judge while you're running around Gotham. And there's nothing you can do about it.
Firefly is too distracted causing fires and explosions on the bridge to keep track of his men until Batman's on the road way fighting them. While there's Fridge Brilliance in that the henchmen in the bridge don't want to give Firefly a reason to set off the bombs, explaining why no one contacts him, if Firefly had been paying more attention to them, he'd have set off the bombs before you could even get to him.
This game shows that Penguin had Candy and Tracey helping him in the past, and both have disappeared by the time of Asylum. The Arkham Stories in City say that Joker and Penguin have been enemies since Joker squirted acid in a waitresses' face. Could that waitress have been one of the girls?
As mentioned above, Bane was able to find Batman's secret identity through something as simple as air radar, technology that's high-tech but hardly impossible to procure. The horror sets in when you realize that if the GCPD had thought to try this, Bruce would've been in jail/dead long before the game.. It may also explain why the Batwings of the earlier games are smaller than the one here: a smaller plane would be harder to pick up on radar.
It's all but stated that the Batwing is the same vehicle throughout all the games, that Batman is just continually modifying and upgrading it. It started out as a prototype stealth aircraft with very few modifications. So Batman likely figured out how it was tracked and corrected it.
We never learn what the Mad Hatter did to the woman he kidnapped, only that she states she won't be all right. What the hell did he do to her?
Raped, most likely. He was established as a rapist in DC Universe. Or maybe he did something worse...
Some of the criminals you beat up say they have kids. So why would they turn to crime? Because it's the only way they can provide for them. Once Batman foils their attempts at robbery or muggings, more often than not leaving them with injuries that require medical treatment, then they'll be saddled with healthcare debts they can't repay, forcing them to go back to crime again. In essence, crime in Gotham is a never-ending cycle, and Batman is the catalyst for it.