Batman: Arkham City/WMG

The Joker's death was an illusion created by the Scarecrow
Three main points:
 * Technically, Batman was the only one who actually saw the Joker die, and lifelike hallucination sequences are already a regular staple of this series. The police might have gotten a corpse that looked like the Joker, but they'd have no way to conclusively verify its identity since Joker has no official legal identity.
 * If that hidden room in the cargo ship and the note about the shipment of fear gas are any indication, it's looking like everyone's favorite mad psychiatrist might play a crucial role in Arkham 3. Now, if he wanted to use his powers to drive Batman insane (which, being the Scarecrow, he's bound to attempt at some point) what would be a good place to start? In Asylum, he figured out that loads of plain old Nightmare Fuel weren't enough to drive Batman over the edge, so now he's trying something different: instead of convincing Batman that his worst fear has happened to him (like he would with most of his victims) he's convinced Batman that he finally crossed the one line that he swore he'd never cross and let the Joker die.
 * Even if Batman didn't intentionally kill the Joker, failing to save him still has some serious moral implications. Batman's entire crusade rests on the idea that not even the worst of Gotham's criminals deserve death, and that he has a responsibility to take a higher path when dealing out justice. When he finally gets forced into a situation where taking the high road isn't an option, he'll be one step closer to becoming just another disillusioned, death-dealing vigilante that the police would be forced to bring to justice...which is probably one of the few things that he's actually afraid of. Convincing him that he killed the Joker was the first step--driving him past the proverbial "point of no return" will be the Scarecrow's goal in the sequel.

Arkham 3 will be a Batman/Spider Man crossover
Is it probable? Well... not really. Is it possible? Next time you're playing as Catwoman, just imagine her with a Spiderman costume, a male's voice, and a web line instead of a whip--their movements and attacks would be practically identical (well, minus the kiss attack, anyway). If they had the rights to the character, the boys at Rocksteady could, at the very least, probably make an unlockable Spider Man skin if they wanted to.

ClayJoker will return.
When you defeat Clayface, they make a big show of him mixing with the Lazarus Pit. Clayface has always been a good actor, but dangerously insane. So, what happens to a man who gets himself perfectly into the mindset of The Joker, only to get mixed with an immortality, but insanity, causing chemical? I have no idea, but I would guess a bit of Mode Lock in the mind of the last crazy bastard he got into the mindset of. So, Joker can be dead, but Clayface can be The Joker with just a bit of memory loss (easily done, seeing as he got electrocuted and mixed with a Lazarus Pit) and a bit of mode lock. Plus, how symbolic would it be for the original Joker to die, only for Batman to create a new one on accident with a large amount of mysterious chemicals?

The third "Arkham"'s villain will be.... Lex Luthor.
My reasoning:
 * A) Arkham City takes a lot of inspiration from Batman No Mans Land, and Lex Luthor was a Big Bad near the end of that arc.
 * B) If Mark Hamill has indeed retired, then Clancy Brown as Lex is the best-voiced villain out there.
 * C) It would allow Rocksteady to prepare for a possible future Superman game.
 * Possibly. For now, it looks like Scarecrow and Hush are being set up as major villains, though they're definitely not the only ones. This may just be a coincidence, but I did notice that the letter in Scarecrow's cargo ship includes a cryptic reference to a "Mr. Fine" who's apparently allied with Scarecrow and helping him plan an attack on Gotham. It's definitely possible that "Mr. Fine" is "Milton Fine", AKA Brainiac. If Brainiac's involved in the plot of the third game in some way, Lex Luthor's involvement is pretty much inevitable. Hell, Luthor might even have been the one who wrote the letter.

The part of Gotham from the last game's opening will appear.
Given that Bats drove through en route to Arkham, it makes it'll be part of Arkham City.
 * Semi Jossed; We can see Arkham Island from the east side of Akham City, but the bridge that connects it to the mainland leads to a different part of town.

The Tomorrow Knight will make an appearance.
Even if he is limited to PvP/ Multiplayer/ New Game+. He'll also be a gamebreaker.
 * It could be an alternate ending where the villains win and thought they killed Bruce, but did kill all of the others(Dick, Tim, Barb, etc.) so Bruce goes into hiding for fifty years and then he has a son named Terry and trains him to take the city back.
 * The Batman Beyond suit WILL appear in the same. As an alt skin for Batman.

David Kaye will voice Hugo Strange
Ok, so this is more of an educated guess than a real wmg,since he has voiced other characters with similar voices before.
 * Jossed (see below).
 * That's debatable. (Also see below)
 * Methinks Kaye will voice a villain that hasn't been announced yet, who will occasionally say yes in every scene, yeessss...
 * Turns out he's just replaced Tom Kane as Commissioner Gordon, even though Kane still voices Quincy Sharp.

Either Christopher Lee or Corey Burton will voice Hugo Strange
Similar to the above WMG. A lot of people were under the impression that Christopher Lee was voicing Hugo Strange. If that isn't the case, then Corey Burton (who played Lee's characters a few times) is voicing him.
 * Corey Burton confirmed.** Granted, I do think it is Corey Burton, but IMDb, like Wikipedia, can be edited by anybody and people have put up false info on the site before during the time before a products release--case in point, until it was reported otherwise, it said Arleen Sorkin would reprise the role of Harley Quinn for AC and that Kevin Conroy would reprise the role of Batman for the Batman: Year One film. So until we know for sure (mostly from something with a source or after the game's release), take it with a grain of salt.
 * Confirmed for real.

The Bat-creations of Grant Morrison will be involved. Somehow.
No real reason. Just Rule of Cool.
 * Semi Jossed? We have some references to Jezebel Jet hidden around Arkham City (there's images of road signs and the like) complete with references to Joker's red and black motif in RIP, but alas, no Professor Pyg or Dollotrons, and no Flamingo carving people's faces off.
 * Well, there's also

Calendar Man will be behind everything
Calendar Man will retain his Hannibal Lecter traits and will be manipulating everything for his own gain. User:Kimota: (this is a prediction so like Doncallmewave I'm signing this)
 * I'm going with this. But I'm vouching for a more involved approach. I reckon he's snapped and he's trying to turn however long a time-period this games lasts for in-game into a holiday. You know, like a "Mourn-Batman-after-his-excruciatingly-painful-death-at-the-hands-of-Calendar-Man-who-is-no-longer-a-joke-of-a-villain Day/Week/Month".User:Wargle (Signing because I want everyone to know that I also want to spread the word of the Calendar.)
 * Jossed. Calendar Man's little more than an easter egg.

The Music Meister will be in the game

 * No reason I'm just putting it out there because nobody will see it coming.
 * He'd better make everyone erupt into a Bat-Chorus of "Welcome to the Jungle" during the opening.
 * This must only happen if he's once again voiced by Neil Patrick Harris.
 * Failing that, he could pop up during the end credits and sing us off, GLaDOS-style.
 * Jossed. There is a Credits Song, but sings it.

The various Shout Outs/Mythology Gags from Asylum will mean that they will be in the sequel.

 * The reference to Firefly's exploits say that he's at large in Gotham. As the sequel takes place in Gotham...
 * Ra's 's body disappears.
 * Talia, at least, is confirmed.
 * Confirmed.
 * Two Face is robbing a bank.
 * Confirmed.
 * Joker released Scarface.
 * Sharp claimed at the beginning of the first game that the Ventriloquist was out and reformed. Then again, he said the same of Two-Face...
 * Scarface does pop up with Joker in one of the tie-in comics.
 * Scarface (or half of him) is in the Penguin's museum.
 * And some of the story pieces unlocked by obtaining the Riddler trophies explain that
 * Injustice Gang is back according to the same paper that references Firefly.
 * Mad Hatter has a display set up in the Gardens, implying that he's free, but doesn't show up in the game.
 * Confirmed
 * Mr. Freeze escaped before the time the game takes place.
 * Freeze is confirmed!
 * Clayface was pretending to be a cop (but still in his cell) back in Arkham, and since everyone from Arkham Asylum is being transfered to the City...

Arkham City is confirmed to have multi-player... of some kind. Possiblities:

 * Commissioner Gordon:
 * Hey, the first game mixed things up immensely, why not have a section where the player has to pull a completely different playstyle by forcing them to play as Commisioner Gordon?
 * Third person thug killing? YAY!!!!
 * What do you mean "forcing them to play as Commissioner Gordon"? I'd willingly play an entire game about Gordon.
 * Like a Gotham version of L.A. Noire?
 * If I were one of the Dev's, I would totally make a side level where you do this. Only all Gordon does is deal with paper work in it.
 * I'm incredibly thankful you're not a game developer then...
 * Maybe it will follow a different Gordon.
 * Or just give our Gordon a crowbar.
 * Alternatively, seeing that the game is set in Gotham proper, you could play as Robin and Batgirl on occasion. This troper would be thrilled to see Cassandra Cain's version of Batgirl in the game.
 * Judging by the fact that Oracle is heard in the first... I would say Joker has already crippled Barb. Batgirl is now Oracle.
 * Which means Cassandra Cain or possibly Stephanie Brown (unlikely since she started as Batgirl since Bruce died) is Batgirl.
 * Note: Alfred will be Mission Control for (at least part of) the game, as Oracle is missing. Hurm...
 * I think it's just too dark to have us playing as Robin... then again... I'm imagining what he would like like. It would be hard to pull off, but if they can do it well, it would be awesome.
 * If you think Robin couldn't fit in the Arkham Asylum setting, you haven't kept up with his comic book. Just because he has red and yellow in his costume doesn't mean he can't be badass.
 * Catwoman, me-wow! We know she's in the game, we know Bats decides to rescue her from Two-Face, why not give her a few levels, or even a two-player co-op mode?
 * Alternately, why not have duo levels with the also-confirmed Talia Al-Ghul?
 * What if there's no co-op, but PvP multiplayer options? You could have Batman, Joker (as seen in the Bonus Level of Asylum), Two-Face, Catwoman, etc., all competing.
 * Word of God has confirmed that Catwoman, at least, will be playable.
 * Robin has also been confirmed to be playable. However, he's a preorder bonus for Best Buy.

The Joker will die for real in Arkham City.
As I've heard, Mark Hamill is going to retire from the role of the Joker after this game. In the trailer he seems seriously sick. Perhaps his part of the plot revolves around how he's dying, and planning to take the city with him. That's pretty much his thing.
 * Kevin Conroy compared the tone to Batman Beyond: Return Of The Joker. Now, perhaps he was giving us a hint as to what the Joker is planing.
 * Oh God! The Joker's gonna torture Tim Drake again!
 * Somehow, I think Joker's going to finish what he started with Barbara... She has been kidnapped prior to the sequel and it's why Alfred has taken over.
 * To be fair, Hamill has said it was his last time as the Joker twice before...
 * Hamill's said that it may not be the last time he voices Joker after all, so maybe he won't die.
 * Well technically it might be apeearing in flashbacks in the next game or some other form of appearance. I really hope they reinact the Joker's death from The Dark Knight Returns

Dr. Young will return as a villain.
Sadistic plans Gone Horribly Wrong, multiple threats from assorted psychopaths, access to money, science background, what's preventing her from completely snapping?
 * The fact that she's dead.
 * Ra's Al Ghul. Lazarus. Pit.
 * And he'd have what incentive to revive her considering how stingy he is with the pits?
 * Not to mention he does have standards despite being a villain, so the whole Titan thing might not be his cup of tea. And he's got money to spare, so that wouldn't matter to him.
 * Jossed. Young isn't resurrected.

Mayor Sharp's plan is to blow up/gas/burn/or otherwise kill everyone in Arkham City.
If the Spirit Of Arkham notes are anything to go by, he really wats to kill everyone who would be in there, after all...
 * This may be the origin for the Joker's mysterious infection, and Batman's nosebleed in the promo images.

Time Travel Twist: In Arkham City Batman will team up with Batman.
Future!Batman will be pursuing a future villain who travels back in time to make sure Present!Batman dies in Arkham City. The two Batmen meet and after the standard Let's You and Him Fight scenario ends they team up to make sure Present!Batman makes it though the game alive. During the team up Future!Batman tries to ship Present!Batman with Catwoman too make him happier and less bitter in the future.
 * Jossed, although

Mad Hatter will feature prominently.
They've played the Scarecrow card once already, but Mad Hatter is also capable of warping what you think you know, through his mind control. This could make for some very wonky levels indeed.
 * Hoping that this happens so hard, just saying.
 * Seconded. You don't want to just repeat the Scarecrow gimmick, but the idea behind it was awesome, and as noted Tetch is all about the mind. Also he's incredibly underused.

The game will take place on a holiday.
Calendar Man has been confirmed to appear, and those are the only times he acts. Possible holidays: Then again, maybe Calendar is just trapped in the ghetto and wants to get out so he can go back to using his gimmick properly.
 * With no snow on the ground, Christmas and New Year's are unlikely.
 * Thanksgiving is possible.
 * Valentine's could be amusing for Catwoman, but lacks interplay with most of the Rogue's Gallery.
 * Joker would love April Fool's Day.
 * Two-Face likes the kind of warped justice symbolism he could get by executing Catwoman on Independence Day as part of a bid to take over Arkham City.
 * Halloween is always classic.
 * It's Bruce's birthday, and Strange told him.
 * Talk Like A Pirate Day.
 * Arkham Day, the anniversary of Arkham City's grand opening.
 * It's been seen snowing in some videos, though Calendar Man has been confirmed to react to different holidays (wearing a Santa Hat, etc.) depending on the game system/computer's clock.
 * However, it's implied that the only reason it's snowing is because of Mr. Freeze.

There will be at least one major gang other than Two-Face and Joker's men.
What's more fun than a two-way gang war with Bats in the middle? A three-way war with Bats and Catwoman in the middle. Possible other factions:
 * Black Mask.
 * Jossed, he does have a faction (and managed to, as a Riddler trophy reveals) but none of them appear in-game.
 * The Penguin.
 * Some people claim you can see him in the teaser trailer.
 * And he's now been confirmed to appear in the game.
 * Penguin is confirmed to have a large gang presence in Arkham, possibly the largest.
 * Bane, returning from the previous game.
 * Similarly, Scarecrow.
 * Strange and Sharp will probably join the fighting using the PMC contractors eventually.
 * Ra's Al-Ghul.
 * Mr. Freeze.
 * He's at least confirmed to be in the game, and he rarely acts alone.
 * Ra's Al-Ghul.
 * Mr. Freeze.
 * He's at least confirmed to be in the game, and he rarely acts alone.
 * He's at least confirmed to be in the game, and he rarely acts alone.

Batman will go insane this time
Joker will be trying to make him go crazy agin, or Hugo Strange...and they succeed.
 * So...instead of "Scarecrow Hallucination" levels, we'd have "Batman of Zur-En-Arrh" levels? Awesome.

Dating Catwoman will not be with Catwoman or Talia
...but with Harley Quinn. Note this promotional image...
 * I dunno, kid. Kinda looks like she's scolding him for always beating up Mr. J.
 * Jossed, given

There will be more then one ending. At least one will be to please the shippers.

 * Everyone will die in one
 * Batman will go insane in one
 * Joker dies in one
 * Happy ending
 * Batman gets the girl ending
 * Batman and Catwoman
 * Batman and Talia
 * Batman and Harley
 * For clarication,

Batman will have an advisor who will turn out to be Clayface.

 * It'd be a good twist, but how would they make it work? Batman's detective vision in Arkham Asylum could identify Clayface when he was disguised.
 * Maybe he'll only appear in cutscenes?

To deal with The Riddler, Batman will enlist the help of none other than Captain Hammer
Bare with me here, In Arkham City, the Riddler's games will be much more tough, so Bats would probably want some help. Now, who does The Riddler look and sound like? Neil Patrick Harris, of course! Now the only person who's "Better Than Neil", ergo better than The Riddler is Captain Hammer! "Captain Hammer: The hammer is my penis!

Batman: ...get out of my city."


 * Except everyone knows NPH is really the Music Meister.
 * Furthermore, Riddler looks like JIM CARREY. Who PLAYED HIM.
 * ...Get out of my city.

Whoever got the Titan at the end of Batman Arkham Asylum will show up...
Only to be dispatched almost instantly by Batman. During Arkham Asylum, he flat out said he was producing more anti-Titan, and like Batman's not gonna carry the antidote around with him at all times.

Deathstroke will show up.
In relation to the above, Deathstroke the Terminator will show up for perhaps one of the most awesome and hilarious team-ups ever. Slade will play the straight-man to Wade's jokes.

If Nightwing is in the game, you will have to rescue him.

 * And in the following cut scene he will be like: I can help Bats! It'll be like old times!
 * And then Bats is like: Get out of here Dick. I'm better off alone.
 * And then Nightwing's like: But we'll be co-op! I'll watch your back you'll watch mine!
 * And then Batman's like: NO.
 * And then Nightwing's all: Why?
 * And Batman's like: I'M BATMAN.
 * And then Nightwing's like: Okay *leaves*
 * But then we hear him chatting with Alfred in the Batcave.
 * And then Alfred leaves to do butler things, and Dick takes over for a bit.
 * Until Batman gets sick of the comments about his love life, and turns off the comlink.
 * Which then leads to a plot point where he misses information due to being unreachable.
 * Wait... Are we talking Bruce's lovelife or Dick's here?
 * Why not both?
 * Jossed: Nightwing is DLC but has no voice actor.

The game will culminate in an Enemy Mine collaboration

 * The words "All In" in the trailer seems to imply some sort of team-up. To take down Sharp and Strange, Batman will need to enlist the help of not only allies like Nightwing or Gordon but members of his rogues gallery as well, like Catwoman, Joker or Freeze since the villains will probably want to get out of the quarantine and want a chance to take down Sharp. In fact, it may just be The Joker who kills Sharp in a suicide attack, with them never finding his body (a good excuse for Joker to be out of the future games with some ambiguity).
 * Jossed unless you count Catwoman, who's really more of an Anti-Hero at this point anyway.

Prometheus will make his video-game debut.

 * As The Dragon to Penguin. Using memory discs of previous Bat-rogues and counters.
 * Nope.

Harley picked out her outfit to take Draco in Leather Pants literally.
It's working.

The Joker isn't sick.

 * Just watch the second trailer.
 * According to the third trailer, there's plenty wrong with him.
 * He's speaking more in the "I'm completely snooker-loopy" kind of way.

Hugo Strange is "The Spirit Of Arkham".
Well, not literally. But the first issue of the "Arkham City" tie-in reveals that now-Mayor Sharp is being stage-managed by a mysterious off-stage psychiatrist, heavily implied to be Hugo Strange, who he's been seeing for years. Strange either picked up on Sharp's preexisting resentment and fear of the inmates of Arkham and intensified it through conditioning until it became a virtual psychotic break, or programmed Sharp with the 'Spirit of Arkham' persona in the first place in order to make him malleable and easier to control.
 * They seem to be leaning towards confirming this, at least in parts. The second issue reveals that Sharp's personality is basically just a blank slate waiting for a commanding enough presence to give him direction.
 * Played with; it's confirmed that Strange used Mad Hatter's mind control technology to induce Sharp's split personality, but it's not confirmed whether the Spirit of Arkham was directly created by Strange.

Rob Paulsen will lend a voice to the game.
And he'll be Mr. Freeze's Dragon. Likely a Large Ham for better contrast.
 * Jossed.

The final boss of the game will be .
And you'll fight him as Catwoman.
 * Oh man, that would be awesome!
 * Well, she's screwed.
 * That's one way to beat him.
 * Jossed. Catwoman is only playable with the Online Pass. The final boss is.

There's a Batcave under Arkham City as well.
Because he's just that prepared, however this time it'll be based on the brightly lit bunker from The Dark Knight
 * And it will be blown up, possibly collapsing part of the city above.
 * Jossed. However there are ruins of Old Gotham, and the Zeerust-tastic Steampunk metropolis that is Wonder City.

Strange/Sharpe's scheme will be Hijacked By Joker.
Because it's Mark Hamill's last appearance as him! Also, it would take more than a city full of rival supervillains and PMCs to stop him stealing the show!
 * It's not his last appearance as him, though. Hamill has confirmed via Twitter that this may not be the end.
 * Hamill indicated last time that it may be his last go as the Joker as he thought he'd done everything he could with the character, but changed his mind when he got a look at Arkham City's story/script. So basically if people keep giving him good material he seems happy to come back.
 * Jossed. Joker's running his own scheme, but it has little, if anything, to do with Strange's plans.

Penguin's "partner" is Killer Croc.

 * There's something very Jabba the Hutt about this Penguin. And Croc would be the perfect Rancor.
 * As it turns out, Penguin's "Rancor" isn't Killer Croc..

The ending will involve a battle between Batman and Hugo Strange...
With Strange attempting to 'replace' Batman... literally. With Batsuit and everything. If most of the more recent interpretations of Strange are anything to go by, he'll end up suffering from the delusion that he is Batman.
 * Additionally, the leaked achievement "I'm Batman - 10G" will not be awarded for completing the tutorial/starting the game, as it's small Gamerscore reward and high place in the achievement listing would suggest, but for encountering Strange in his Batsuit.

The Ridder's going to suffer an epic Villainous Breakdown
...and it will be awesome!

Similarly, the reason that Riddler is so much more menacing in this game is because of last game's Villainous Breakdown
Think about it, with the nature of some of the challenges in Arkham Asylum, you'd think Nygma put a lot of preparation into everything. It was his greatest effort to fool Batman, and when it failed, he kind of...snapped. The gloves were off, and he went from silly trophy-hiding Riddler to kidnapping-innocents-and-putting-them-in-death-traps Riddler
 * Confirmed.

Harley Quinn will pen and/or read a letter beginning with "Dear Mr. J."

 * Her new voice actor is Tara Strong, it's either that or a Fairly Oddparents reference.
 * With Grey Delisle as Catwoman, the latter would be more likely.

The ultimate villain and The Man Behind the Man for Hugo Strange will be
Not exactly a ridiculously out-there guess, I know. No evidence at all, I just say this purely because a)  is slated to appear, b) it's the only villain who could be seen as a "bigger" threat than the Joker (who won't like that, chances are) and c) it's be awesome.

Oracle has been kidnapped by Strange.
That's why Alfred is the Voice With an Internet Connection. Strange knows Batman is Bruce, what's to say he hasn't figured out the identities of the rest of the Bat Family? Barbara is his insurance if Batman looks like he's going to win (and you know he will).
 * Jossed. She shows up halfway through the story having been occupied with other things previously.

Jack Ryder will become The Creeper.
Ace Chemicals is located in Arkham City and Ryder appeared in a gameplay video where he was saved by Batman. If he could have changed into the Creeper he probably would have, so it's a safe bet he'll end up dunked in the same chemicals that Joker fell in and become an unpredictable ally for Batman, maybe even being briefly playable. The bios from the first game have already been shown to not be canon in the case of Strange, so it's a possibility.
 * And the city would be much more colorful and "Bruce Timm-esque" when you play as him, as well as comical, rather than gritty or serious. It would also come after an incredibly serious moment.
 * The game will re-create the scene from his DCAU appearance where he takes out several Joker goons, as well as Batman himself, without missing a beat. Combined Crowning Moment of Awesome AND Funny?
 * In fact, Ace Chemicals can be glimpsed briefly in the same gameplay video Ryder appears in, less than two hundred meters away from where Batman saves him. If he's that close already...
 * Jossed, for this game at least. There's always next time, though...
 * Although Vicki Vale mentions the Creeper in the second Quincy Sharp interview tape. So looks like Jack Ryder's already been changed.

Red Hood will appear in game if only as a cameo.
Talia Al Ghul is in the game and Tim Drake is in challenge mode so why not have the second Robin show up as well.
 * Because the first Robin would be far more deserving.
 * Well, Nightwing has been confirmed as DLC, so he'll probably at least have a cameo.
 * Jossed.

The Titan formula had a bad reaction with the chemicals that created Joker.
Unlike the mooks of the last game that Joker was experimenting on, Mister J. had already been transformed by the vat he fell into at Ace Chemicals. The two mixtures resulted in his much more horrific appearance at the end of the first game and are now slowly killing him. This will only make him more dangerous, of course, as he's either desperately searching for a cure, resolved to killing or breaking Batman before he dies or both.

Alternatively the titan formula is curing the Joker.
Just as Dr.Young intended to do with it from the beginning. The bad reaction is completely psychosomatic, heavy on the psycho.

Mr.Freeze will be injected with the titan at some point
And turn into a giant ice monster. That's never been done before in a superhero game right?
 * Jossed. Something like that would've likely caused a large amount of Nerd Rage, anyway.

Ivy will have a bad reaction to the Titan.
This will somehow cure her or turn her into the giant killer plant Joker wanted.

The Penguin having ... Will come back to bite him in the ass.
He's trying to control a nigh-unstoppable beast, and since that beast is chained up and being electrocuted...

The last villain trailer we see will be of Talia Al Ghul

 * Considering that we only have one picture of her to go on, there's a good chance that before the game hits stores, we will see why we should care that she's there. No, acting as one of the woman that Batman has to decide on who to hook up with does not count.
 * Jossed, as that's basically her role.

Scarecrow won't be in the game...
But Scarebeast will. It also explains why his VA, assuming he wasn't lying, isn't reprising his role as Scarecrow.
 * Jossed. All you see of Scarecrow in-game is his mask, which is the solution to a Riddler Challenge.

Besides Tim and Alfred, there will be references to much more of the Bat-Family.
Dick, Cassandra, and Stephanie, amongst other possibilities. Maybe even Batwoman.
 * Nightwing is a DLC character.

Superman will get referenced, even if only obliquely.
...as foreshadowing for a potential Superman-Batman teamup game. Because Supes really needs a game to redeem himself from the whole Nintendo 64 fiasco.
 * Rocksteady is planning on making a Superman game after Arkham City. Just throwing that out there.
 * Confirmed.

Harley Quinn will act as the Catwoman beating Batman while Joker looks on.
Only if the guys at Rocksteady are Avatar fans of course.

Mr. Freeze is the reason it's snowing throughout Arkham City.

 * Confirmed.
 * Well not really. It's the middle of Winter, however the goons have noticed that it's getting colder every year. They blame Freeze for THAT.

Ra's Al Ghul will be the main villain of the third game.
Talia's supposed to appear in Arkham City, but the villain roster is starting to get pretty full, so maybe Talia's appearance is meant to foreshadow some bigger scheme by her father some time in the near future.

Deadshot is working for Hugo Strange
It's been mentioned he managed to have his Hand Cannons and a Sniper Rifle smuggled into Arkham City, but given that even Batman can't get things in and out of the city easily, is it not more plausible that he had help from Strange?
 * Confirmed.

The mysterious chemical Batman tries to get from Mr. Freeze in his debut trailer is the cure for the Joker's disease.
Of course, it's probably also the cure for Nora's, which is why Freeze isn't too keen on parting with it.
 * Partially confirmed.

Alternatively, Mr. Freeze's mystery chemical is the key ingredient Batman needs for his freeze capsules.
If you subscribe to the "Joker isn't really sick at all" theory, this is the next most logical thing Batman might need the substance for. As for why Freeze wants to hang onto it, it could be that it will allow him to keep Nora on ice without the need for so much heavy equipment.

OR Mr. Freeze wants titan
It would explain why Batman isn't willing to bargain with him since he wants it in as few hands as possible. And Freeze plans to mix it with other stuff.

Rather than Joker, Hugo Strange will comment on Batman's performance in the Challenge Maps.
It would make sense. The prequel comic mentions Strange is trying to study Batman's moves. What better way to study him than to set him up in an arena with a bunch of Mooks?
 * Jossed. The Riddler provides the commentary.

Rocksteady's next game will be The Punisher
Don't act like you don't love the idea
 * Jossed before it even happens. WB Games, the parent company for Rocksteady, is also the parent company for DC Comics. Making a Marvel game would be working for the competition.
 * There have been DC/Marvel cross-overs before

Hush will be the main villain in the next game.
He's already altered his face to look exactly like  and intends to use this to ruin his reputation.
 * For bonus points, Hush obviously hasn't happened in the Arkhamverse, leaving Rocksteady plenty of freedom to do whatever they want with Tommy Elliot. Can anyone say Superman boss-fight?

Its a long shot yes, but Batman has had crazy plans before.
 * Well, it could certainly be a subconsciously executed Batman Gambit.

Batman will end up adopting .

 * And the sequel will be you playing as

The Arkham Asylum and Arkham City games are in a divergent timeline from Chris Nolan's The Dark Knight Saga

 * Asylum would take place 9 years after the Dark Knight, Arkham City is 10 years after The Dark Knight (making Batman 34 and 35 years old in the games). There are two timelines opened at the end of The Dark Knight, the one we see in the movie where Two-Face, and a separate timeline where he lives and is taken to Arkham, the hundreds of criminals he put in prison as Harvey Dent would have been released due to Dent becoming a killer and those 500-or-so criminals would likely go on to become the many supervillain henchman we see in Arkham City. This, in turn, would cause the people of Gotham to put more faith in vigilantes like Batman. Robin, Batgirl, Nightwing, and other heroes like Huntress and Creeper would soon follow. There are small tidbits that are open to the interpretation that these games are in canon with the movies. Here's a list of any connections between the films and the games:
 * The Batsuit being armoured, the glider cape, and being able to bend an enemy`s gun barrel using the hydraulics built into the suit (a new addition to Arkham City, but it's right out of TDK), and the concept of detective vision comes straight from TDK also.
 * Two-Face's general look
 * Joker's suit and painted-on red smile
 * The crashed monorail (from Batman Begins)
 * Scarecrow's mask, as well as his obsession with poisoning Gotham`s water supply using the pipes under the asylum (again, from Begins)
 * Croc's appearance (similar to his look from Batman Gotham Knight)
 * The flashback from Batman Arkham Asylum of Bruce losing his parents and meeting young Gordon at the police station
 * The general look of Gotham's Narrows
 * Ra's having a burned corpse in Arkham Asylum
 * Batman drinking from the cup before having to undergo the  is similar to the start of Bruce's training with Ra's in Batman Begins
 * The Riddler looks a bit like David Tennant, who many people speculated would play the Riddler in The Dark Knight Rises (it is a bit of a stretch, but I just can't help noticing it, especially because of that fake poster- search David Tennant Riddler on Google Images, then click on the first link you see).
 * It really wasn't a stretch, he said if it was at all possible he would play the Riddler in a Batman movie.
 * It really wasn't a stretch, he said if it was at all possible he would play the Riddler in a Batman movie.

By the time of the third game, Harley will be one of Gotham City's premier gang leaders
, the Penguin has been humiliated and imprisoned, Two-Face has also probably lost a lot of credibility after being shown up by Catwoman so many times. Even Joker's own men mentioned Harley wouldn't be able to crack leading a gang for even a day, but what if, possibly with Ivy's help, she managed to take a level in badass and prove them wrong?
 * Going off of this and Azrael's ominous comments, Harley's plan will involve burning down Gotham with Batman in it.

In relation to the WMG above, Rocksteady will make Batman Inc. as their 3rd game
At this point, they're gonna be going for a big finish for the third game.

The third game will be a straight-on adaptation of the Hush storyline

 * It only makes sense.  appears in a side mission and is still on the loose, Scarecrow is still at large and swearing revenge, and the Riddler will always try to one-up Batman. These three characters are the masterminds who work together in the first Hush story. Add to that, all of Gotham would be playable, Nightwing, Robin, Catwoman, and Huntress would appear in the main storyline, and Supes and Lois would make appearances.

The next game will be based on Cataclysm/No Man's Land.
Two things lead me to this theory: 1)  makes reference to Gotham "burning, and you will burn with it." which implies a major disaster is going to occur, and 2) seriously, how else are they going to get any bigger than this? Bonus points if they make Robin/Nightwing/Huntress/Batgirl into playable characters with branching campaign arcs!

Batman genetically modified himself so that his facial hair grows faster
Think about it! It's the perfect way of disguising his jawline. Bruce Wayne is thrown, clean-shaven, into Arkham City, about eight hours later, the Batman has the beginnings of a beard! Bruce is probably Genre Savvy enough to know that exposing his jaw makes him easier to identify, so he could've messed with his genes in an effort to throw people off the scent.

Killer Croc will return in the next game

 * He'll be stashed out in a quarry. Once Batman comes closer and closer, he'll throw a rock at him.
 * It'll be a big rock too.

The Scarecrow boat easter egg will do something on halloween.
The boat that you can find in the docks has a drugged goon and a shipping invoice in it. If you look closely at the invoice the total cost of shipping the roaches came out at 560, 550. I assume I'm not the only one who tried to use it un the cryptographic sequencer, because it looks like the radio frequencies you've been using through the entire game, but it didn't do anything. I really hope it isn't a Red Herring, so I'm guessing it's gonna do something on halloween.
 * You can change the system clock to find out whether this is true. However, considering your previous encounters with him in Asylum, I dare you, because I am not taking the risk of possibly proving this theory.
 * Jossed.

Clayface also wanted to become immortal. And he did.
When the offer for immortality is made, it is Clayface who accepts it. Joker would also want to become immortal for obvious reasons. Seeing what happens at the end of the game, Clayface got what he wanted.

Riddler will ascend to being the Big Bad of Arkham 3
In Asylum, Batman solved his riddles, and he vowed to return with even more taxing ones (in between getting whupped by the cops), he made good on that promise in City, but Batman still managed to beat him. Riddler isn't the type to let it end there, so surely the only thing left to do is find out the identity of the Batman and crush him, once and for all.

Batman let his alter ego Bruce Wayne get arrested and sent to Arkham City on purpose.

 * This is pretty much a gimme. This is Batman who has millions of plans for every doomsday scenario possible, and a few that aren't. You don't think he couldn't have avoided being arrested if he wanted to? No, his plan was to get arrested so as to get inside Arkham City without getting shot at by Tyger. His choice of where to have his press conference (the front gate of Arkham City) is very conspicuous as Tyger has to go all of a hundred feet to put him inside Arkham City. From there it was a simple matter of having his equipment sent to him so he was more or less free to roam Arkham City without much interference from Tyger.
 * Nope. At the beginning of the game, having gotten into contact with Alfred, he's asked whether being arrested was planned, but it was beneficial since he got some face-time with Hugo Strange and learns about Protocol 10. Obtaining certain Riddler trophies and the like also tells us that Bruce Wayne's anti-Arkham City movement was genuine and something Batman proposed to Commissioner Gordon to fight Arkham City legally and publicly, since Sharpe had ignored Gordon's private protests. As such, whilst it benefits Batman in that he's able to bring Arkham City down after stopping Protocol 10, he probably never intended to get arrested. As for putting the press conference directly outside the gates, that's akin to any protest - You don't protest something by being in front of another site entirely (think Occupy Wall Street).

Arkham 3's real villain will be Red Hood
The game will start with Harley controlling the remainder of Joker's forces with some extreme competence at Ace Chemicals(maybe putting her baby in the chemicals to make a new Joker). Batman is in the scaffolding waiting for the approtunity to strike when someone else arrives and starts beating and maybe even killing Harley's men all the while wearing a red mask. When the individual goes to kill Harley Batman intervenes. They fight and are extremely well matched until Batman thinks of a way to have the upper hand but accidently causes the new red hood to fall into the chemical vat. What comes out is the new crown prince of crime setting the rest of the game up. Alternatively the new Red Hood is wounded and leaves a blood sample behind. Batman analyzes the blood but finds the batcomputer's data for the match is corrupted and he can only get a small DNA match that can connect to any number of criminals in the city but there's the enzyme from Ra's al ghul. He goes back to the Lazarus Pit Chamber to find certain people alive and well(Ra's and Talia) but finds no match in either of them, but does learn that they had put someone he's familiar with in the pit. Red Hood attacks again and is again wounded. Batman has a greater DNA match and decides to eliminate anyone from the list that he's isn't more deeply familiar with then eliminates those that are far to unlikely to still be a suspect. He continues to investigate and soon comes across further evidents when the Red Hood has captured Robin. He comfronts the Red Hood who tells him the only real way to save the boy wonder is to kill him. Batman fights Red Hood and removes his mask revealing no one else but Jason Todd.

Every theory about the third game mentioned in this GamesRadar article will be true.
Seriously, it's as though they've collected every possible Wild Mass Guess about the third game into one article and figured out how to make them all sound plausible.

In the Arkham Verse Nightwing and/or Robin covered as Batman while he recovered from Bane's assault.
Either sanity prevailed, or Alfred/Oracle put their foot down.

.
We know he likes that movie because he quotes it in the first game, plus it just seems like the kind of thing he'd do. "The Joker: Batman may look like an idiot, and talk like an idiot, but don't let that fool you: he really is an idiot!"

Firefly will play a large role in Arkham 3.
Who do we know of that can cause a huge, city-burning fire? If Harley really wants to burn the whole world, she could hire the services of Gotham's resident pyromaniac. He'd also be Nightmare Fuel, since his MO is that he can "see things" in the flames; the player could probably see his POV sometimes.

Batman sometimes kills people during fights, but doesn't realize it because Oracle programmed the Batsuit to show them as unconscious.
Think about it. How could Batman have a 100% success rate with no killing? He has no way of knowing if a random henchman has a weak heart, a fragile skull, or other ailment that would make a regular Batman punch fatal. Throw in gadgets and predator mode and it's even worse-- what about the people who end up unconscious face down in water or strung up from a gargoyle? Now, think about Oracle. She is much less concerned with human life in this continuity-- she openly wonders if Bats should bother going after Deadshot, since he's taking out residents of Arkham City and she figures they're all bad people anyway and she doesn't seem bothered that Bats may have been tricked into killing people in the Identity Thief side mission. It's Alfred, not her, that forces him into stopping Protocol 10 instead of rushing after Talia. She just made a slight tweak to the cowl-- if Batman kills somebody on accident, they show up as unconscious. She knows that Gotham needs Batman and he would quit if he knew he killed somebody.
 * That's arguably the best explanation I've heard for why Batman's brutality only renders people unconscious.
 * Doesn't seem likely to me. Remember, Lucias Fox exists in this continuity, so he's probably the one making all the tech, including the Detective Mode Vision thing. Oracle is great at hacking and gathering information, but sneaking in a tweak like that under both Batman and Foxes nose doesn't seem likely. I mean, come on... it's Batman. He'd know.

Rocksteady will go even bigger for the third game.
All of Gotham will be playable, you'll have the Batmobile to use to get around, side missions will be given out by Jim Gordon who will call you with the batsignal. This will include almost the whole Rogues gallery, who will commit crimes for Batman to solve, independent of the main plot. Batman will call in all of his allies, and you'll be able to utilize Robin, Nightwing, Batgirl, Catwoman, Huntress, and other allies in combat and in stealth similar to the assassin recruits in Assassins Creed Brotherhood. The game will also support co-op multiplayer, friends will be able to take over an ally, allowing for one of the first ever co-op stealth games, allowing you to set up joint take downs, and combos.

In Arkham 3, you will have several "campaigns" depending on which character you play.

 * As Batman, you'll deal with Hush, Scarecrow and the Riddler working together to bring Gotham to its knees:
 * Hush by slandering Bruce Wayne's reputation and taking from him everything: industries, charity associations, a huge part of Gotham will go down with Bruce Wayne if he's convicted of the crimes Hush commited.
 * Scarecrow will try to reduce Gotham's citizens to a bunch of rampaging terrified lunatics.
 * The Riddler will be back with a vengeance, and help the other two because the best victory over the Dark Knight is completly destroying what he fights so hard to protect: Gotham City.
 * That Campaign will be about saving Gotham's Soul, its Hope (symbolized by Bruce Wayne) and Humanity (the citizens).
 * As Robin, you'll investigate on a possible return of the League of Assassins, because he's the only other in the Batfamily that Ra's Al Ghul respects -he calls him "Detective", like Batman
 * As Nightwing, you'll have to stop Ivy on her "anti-humanity" roaring rampage of destruction. Why? because this troper would love an opportunity for some Oracle/Nightwing banter!
 * As Catwoman, you'll try to find out what happened to Harley, and maybe find out that
 * If the stars align, they may even let us play as the Cassandra Cain Batgirl, or at least let her have a token appearence similar to what Robin got in this game. Why? Well for one thing the poor girl deserves some mainstream exposure by now, but her whole backstory and staunch conviction to her Thou Shall Not Kill beliefs matches up perfectly with Rocksteady's interpretation of the Bat mythology. She may end up having to deal with the more 'conventional' crooks while everyone else is dealing with the super villains: the mob families, Two-Face and Ventriloquist emerging to reclaim Scarface all seem like good candidates.
 * Taking Azrael's Vagueness Is Coming prophecy in AC, all the characters campaigns will combine for a grand finally, Sonic Adventure style, that will result in the near/total destruction of Gotham, and will have even the villains teaming up with the Bat family to save their city.

The above two will both be utalized for the third game.

 * And it will be called "Gotham City" and will mark the final in the trilogy, with an ending (maybe a secret unlockable one) teasing that they'll go on and make a Superman game as their next project.

Strange did not hire Deadshot expecting him to succeed.
The real reason he hired him was to get him killed during Protocol 10. There's no reason to allow a contract killer to roam free when he's rounding up all the criminals of Gotham and. Why else would he need to hire an expensive assassin to gun down the political prisoners when ? This also explains why Batman and Bruce Wayne are listed separately on Deadshot's hit list: Strange wants him to waste his time to ensure he's still in Arkham City when Protocol 10 is initiated.
 * Seems especially likely that Strange hired Deadshot with the intention of getting him killed; If he kills the people on his list, then there's zero chance of them speaking out in the wake of Protocol 10 - where, inevitably, people would have to enter the city to clean up; It also contributes to the idea that, because Strange undoubtedly has footage from the TYGER surveillance stations and could claim Deadshot made his own way in, further making Arkham City seem a failure. So Strange kills two birds with one stone.

Vicki Vale was the Mad Hatter's next target.
When you first see Jervis, he's spying on Vicki and Batman after one of his heroics with her. Though the sidquest shows he's after Batman, I'm sure one of his quotes during the struggle states that when Batman's under his control he was going to send him after "Alice". She's blond, beautiful, and women are slim pickings in Arkham City. With his mind fractured further than before, guess who's getting her own special tea. In the Interview Tapes Hugo Strange get's Jervice's cooperation by showing the Hatter "Alice" for him to keep when he's released. It's possible the "Alice" Was Vicki trying to interview Dr. Strange or Quincy Sharp. It's not hard to see the not-so-good doctor rigging Ms. Vale's arrival in town to keep his promise.

: The new Star Trek movie was never made in the Arkham-verse.
Joker was unhappy with the ending to Lost. J.J. Abrams is most likely exceedingly dead.
 * Maybe not. That line was delivered near the end of the game, when Joker started make a lot of entertainment industry references, to foreshadow . Plus, he never said he didn't like it, he merely acted amused at how it upset others. So, it's just as likely that, in the Arkhamverse, J.J. Abrams is a supervillain. Scary stuff.

One of the sequel's plots will focus on Harley trying to resurrect the Joker.
Most likely the next game will have a number of intertwined subplots, but Harley is most likely going to focus on bringing Mister J back at any cost, if she's given even an inkling about the possibility. She could commandeer cryotechnology from Mr. Freeze, and start a project to excavate the Lazarus Pit back to functional condition. Of course, if she succeeds, the result will be an abomination - a monster hybrid of Joker and Clayface.

Oracle was late to the party because Barbara Gordon needed to ditch her bodyguard.
Commissioner Gordon just saw TYGER guards snatch an influential billionaire from a podium in the middle of a live press conference. Gordon probably wouldn't put it past Strange to snatch his daughter as punishment for his own opposition to Arkham City, so he assigned someone he trusts to protect Barbara. This was inconvenient for her since she couldn't lead him/her to her Oracle layout so she had to take the time to ditch them first.

Scarecrow did have a presence in Arkham City.
Between the hidden messages (most likely from him as they triangulate between the Gotham City radio tower, his mask on the bridge and the hidden boat), the boat itself filled with insects and the possibility of hidden Scarecrow thugs, there's plenty of evidence Crane is Not Quite Dead. Additionally, the insects found in the boat are found in multiple places around Arkham City (Wonder City, Hush's lair, some of the Riddler Hostage rooms). Maybe Scarecrow's been using them as carriers to spread the effects of the fear toxin?

The sequel will have a fight between the two Azraels.
At some point Michael Lane and the Order of Purity will break off from the Order of St. Dumas and Lane will end up going rounds with Jean-Paul Valley.
 * Why are we assuming Valley exists in the Arkhamverse? It does seem likely that Azrael will fight both against and beside Batman at different times, though.

There is a very well-hidden secret in the game.
Much like the "Warden's Office" secret in Asylum, Rocksteady has put in yet another nigh-impossible to find secret. It also gives us a big clue for the next Arkham game. Hopefully, if it does exist, they'll throw us a bone after a few months if nobody can find it.
 * I think that may have been meant to be the Scarecrow hatch this year, it was just found much faster than they expected. I mean think about it, compare the two - in one, you have to spray a specific spot on some wall with three bits of explosive gel and blow it through. In another, you have to divebomb onto a hatch on some seemingly random boat, and then pull out the cryptographic sequencer. They're both rather random things to do, yeah? Also, similarly to the Warden's Office secret, what you find in Scarecrow's hidden hatch appears to relate to a villain's plans for the sequel. So yes, I think this was supposed to be the unfindable secret, but - possibly due to the Warden's Office fiasco from before - people have scoured all over Arkham City looking for secrets, and they ending up finding this within, like, a week of the game's release, and now pretty much everyone knows about it.

The Justice League doesn't exist in the Arkham-verse.

 * A lack of a League wouldn't stop Superman hearing everything that's going on from a few million miles away. Though that does raise the question of why he isn't zooming in and kicking ass...
 * Well, the Leaguers do tend to stay out of each others' various cities unless they specifically ask for help. Depending on how long they've known each other in this continuity (if at all), it's not a far stretch to say that Clark would know well enough not to give Bruce unwanted help. For superheroes, it's a big mutual respect thing.
 * As an expansion, we might assume that other superheroes don't exist. Strange is pretty blithe about setting up camps in Keystone City (which would be problematic - Flash's presence means there are almost no homicides, and thus getting public support is unlikely), and Metropolis (which would be insane, since Superman's senses would quickly penetrate Strange's secrets), and even if Strange was too crazy to think that through, Ra's isn't. More thematically, the Arkham games have really focused on the theme of superpowers making people inhuman (look at Ra's fear of what the pits are making him, or Ivy's deterioration between Asylum and City), so a heroic person with powers seems less natural there than in other continuities.

The third gang will start with a massive gang war, and then it will get worse.
Black Mask is practically fated to be in the third game: they've designed a character model and everything. The games have dropped no fewer than two hints about Maxie Zeus, with his cell in the first game and his nightclub in the second. Two-Face ends the game in a position of relative power. Scarecrow is still out there and obviously more than a little upset about his run-in with Killer Croc. Azrael has warned Batman that Gotham is going to go up in flames.

In the third game, Harley takes over the League of Assassins.
Hey, they're leaderless, and Harley needs some thugs. It's a good fit.
 * Calling them thugs doesn't exactly seem accurate, and even then why would they join up with the girlfriend of the guy that killed Talia?
 * New leadership for the League does seem likely to come up in some form, though. If Ra's and/or Talia is brought back, that would surely warrant a mention, and if neither is, there's a powerful group of international terrorists guarding the secret of immortality... without a clear line of succession.

The third game will fast-forward to the Arkham-verse's version of Beyond's time
And the Dee Dees will feature prominently in it. Between the Beyond costume and the sandbox approach City takes, it'd make sense.
 * It certainly makes sense, given that the pregnancy is major sequel bait and too big to simply be put in the background of the sequel, and beating up a pregnant woman or a child just wouldn't be a 'Batman' thing to do...It seems likely that Joker Jr. will be going up against Terry. And let's be honest, we all want to be able to fly around a cyberpunk Gotham with Terry's rocket boots.
 * Seconded by User:Alex Sora 89. Not only,  is gonna become... *smirks* Joker Junior.
 * Thirded by The Mighty Heptagon. Alternately, Bruce and Terry will be playable, with the timeframe jumping back and forth to show how past events affect the future. Or Bruce will simply by a Decoy Protagonist. Also, keep in mind that if this theory is correct, there's a solid possibility that.
 * Fourthed. Barbara sounded pretty damn jealous when Bruce first brought up Talia, possibly alluding to their failed relationship in Beyond (I can't think of any other continuity where they got together or even felt any attraction to each other). That being said, I suspect we might not see this till the fourth game since Azrael's warnings and Scarecrow's plot suggest something along the lines of a city wide catastrophe too big to be contained in a DLC. And there absolutely has to be a Boss Battle with Mad Stan.
 * Or, alternately, it'll be resolved in a DLC mission. Just a thought.

In the third game, The Riddler will have reformed and will take the place of Oracle/Alfred.
But won't be able to stop being an Insufferable Genius to Batman, despite being on the side of good.

You can play as Harley and Ivy in the next game.
I just want it to be true.
 * And at some point Ivy will fight Zombies.

Razor is a Butt Monkey with Legacy Immortality.

 * Whenever Joker's gang winds up with a new recruit who is exceptionally clumsy and gullible, rather than just killing him, they give him the tough-sounding nickname "Razor" and convince him that he is a respected and feared member of the gang, when in reality he is simply the gang's Butt Monkey. Whenever Joker expects his gang to perform an especially dangerous task, Razor is always given the most dangerous roles and is frequently left to die. When the current Razor meets his demise, the process begins again and a new Razor is selected. For example, the man known as Razor in Arkham Asylum was left in the room filled with Joker gas (twice!) and was eventually killed during the Joker's test of the exploding gargoyles. Razor's nature as a Legacy Character explains why the death of Razor at the hands of Two-Face is being mocked by a pair of Joker Thugs in Arkham City even though the character is clearly deceased in Arkham Asylum.

The Abramovici twins will be back in the sequel.
They'll be surgically reattached, and working for Two-Face. That guy would LOVE a pair of conjoined twins as Elite Mooks. And they'll be a boss fight!
 * And maybe, they'll get exposed to Titan, too...

Talia will be back, as a proper villain this time.
Ra's couldn't bear losing two of his potential successors on one day, so he gives her a dip in the Lazarus pit. It's not exactly good for her sanity. Maybe she'll even overthrow her father to lead the League of Assassins herself.

Harley Quinn will be the villain of the third Arkham game
In the third game, Harley will want revenge on Batman and will attempt to kill him to avenge the Joker while at the same time, taking care of her baby.
 * She's the main antagonist of her own DLC...

The Main Gang leaders in Arkham 3 will be...

 * Two Face: Pretty obvious really. By the end of the game he controls most of Arkham City and has the Penguin locked up. After the vacuum left behind by Joker and Strange Two Face will have no problem strengthening his position.
 * Black Mask: His cameo suggests that he'll be playing a much bigger role down the line. As the only inmate to escape Arkham City, he's got a very strong reputation to draw in followers.
 * Harley: Next in line to the Joker's empire before her kid grows up. She may have a hard time controlling his goons since they don't seem to show her much respect but she could always use Ivy to strengthen her position.
 * Carmine Falcone: While he's dead in comics canon the Arkhamverse does have tendency to deviate from the source material (since Bane broke Batman's back but this is his first encounter with Azrael). We know the Falcones moved their operations to Bludhaven to avoid being sent to Arkham City, and with the death of Strange and the Joker they may move back in to exploit the power vacuum. Also Calendar Man teases Catwoman about her father, whose been suggested (though not outright confirmed) to be Falcone.

Potential villains to be introduced in Arkham 3 (besides the obvious ones):

 * Hush, Riddler, and Scarecrow. As mentioned before, the prime antagonists in the Hush storyline.
 * Wasn't this supposed to be "besides the obvious ones"? Hush plot or not, those are a heavily foreshadowed introduction, a recurring boss, and the breakout villain of the first game, respectively. They'll be there.
 * Prometheus. C'mon, he's the anti-Batman. Imagine having a boss fight with yourself!
 * Firefly. Azrael already mentioned Gotham going up in flames, and he would make an excellent boss fight.
 * It would finally give the series a chance to intregrate platforming challenges and boss fights, as you chase him around outdoors, trying to catch up with that jetpack.
 * Solomon Grundy, for the sheer fact that he never dies.
 * Man-Bat. If only because fighting a giant bat would be a pretty cool boss fight.
 * Calendar Man, but only on certain holidays. For added replay value. Or "set your system clock" value, anyway.
 * Maxie Zeus. Perhaps an electricity-based Mr. Freeze?
 * The Red Hood. Maybe even make him a player character, just because.
 * Jackanapes. Yes, he's supposed to be Damian Wayne's future child, but he is a gorilla with a machete.
 * Bat-Mite, just so we could have a new Mad Hatter/Scarecrow-type thing.

Clayface never told Joker about the Lazerus Pit.
Think about it. If Joker knew about the place why not go there instead of baiting Batman for a cure he didn't have. He clearly wanted to live but seeing how Harley stole the cure and immediately after that Joker started letting Clayface impersonate him to put up the illusion that he'd gotten the cure and it had worked there was no reason for Batman to be saving any for him. Given he spends his last moments trying to lap the cure off the ground it's clear that Joker wanted to live. As crazy as he is I think if he'd known there was a third option he would have gone to the pit himself.

Freeze will have largely reformed by the third game
His only villainous acts in Arkham City are directly trying to save Nora's life - not in the long-range sense, but from immediate harm at the hands of Joker's thugs. He makes a point of telling Batman "we are not friends," and those two do make a point to threaten each others' lives (for no real reason), but this Freeze has a very good shot at getting out of the supervillain gig, and is a fan-favorite semi-ally to boot.

The Bat-Family (Nightwing, Robin, Huntress, etc.) will be bosses or bonus bosses in The Sequel
They've used pretty much all the A-list villains. People want to see the heroes. Kill two birds with one stone, then, since having the Family as bosses adds recognizable characters without having to go outside the Gotham City limits. Also provides a new and legitimate challenge to Batman, fighting a high-tier martial artist rather than just punks or abominations.
 * Of course, they'll be manipulated in some way; brainwashed by Ivy/Hatter, gassed by Scarecrow, indoctrinated by Cerberus (Nightwing DOES look like Kai Leng...), manipulated by Hush, recruited by the Order Of St. Dumas, or what have you.
 * That would be cool, but unless Rocksteady thinks of a very different way to handle one-on-one fights in the combat engine, it wouldn't be practical for the same reasons we couldn't have a Hugo Strange boss fight.

The third game will take place in a section of Gotham flooded with Fear Toxin.
This would pay off the Scarecrow foreshadowing by making him the Big Bad, andresolve most of the questions regarding a sequel. How can you set the next game in an even larger area than a square mile of outdoor prison? It's a large section of town populated by normal people, but they're all either hiding in terror, or have gone insane enough to attack Batman on the streets. If the villains control the area, why are there so few armed enemies? Only a few civilians, the cops, and Scarecrows own minions would be likely to be armed. Why are these ever-larger problems only reachable by a lone vigilante? All the other authorities are busy maintaining a quarantine to keep the gas contained. And how will Azrael's vague predictions about the doom of Gotham come to a head? The whole city literally being destroyed by its own fears seems to fit the bill.

Naturally, Batman would have a gas mask and thus be immune to the gas, but would occasionally get injected, and then go through Asylum-style Scarecrow sequences until he could get an antidote (and maybe some random hallucinations would occur more and more towards the end of the game, as the trace amounts of gas getting through his filters built up).
 * This actually seems very likely. I'm not sure if this is official yet, but I always took the password to the secret Scarecrow area ("CITYOFTERROR") to mean that Batman: City of Terror would be the title of the third game. If this is the case, a plot like that would definitely fit the title.