TRON: Legacy/WMG

""There's a 68.71 percent chance you're right.""

- MCP

Ed Dillinger Jr WON'T be a villain in the sequels.
Probably a Jerkass anti-hero. It's unlikely he got to be member of the board thanks to daddy's influence: after all, Ed senior's name should be pretty much mud considering his theft of Flynn's games. Junior probably clawed his way to the top, and it's more likely he despises his father for being a talentless thief.
 * Supported by bonus material on the Blu-Ray release. "Junior earned his place. He stays."
 * Possibly subverted by hidden bonus content in "The Next Day". It' revealed that he's somehow in contact with the Master Control Program... although he seems to think it's his father.
 * My theory is that it is his father. Ed Sr. has discovered the grid, and is now the new Master Control Program.

Tron isn't dead.
We did not see him de-rez. Also, Tron has survived multiple "deaths" (The destruction of the solar sailer in TRON, as well as getting knocked off a ledge in Legacy AND his ship exploding), qualifying him for "character with the ability to survive certain death."
 * Considering that he never derezed and that he lit back up with "good" colors after hitting the water, I see no reason to think that he's dead in the first place.
 * If we consider how the grid works in TRON 2.0, what seems water in the grid is actually a pool of concentrated regenerating energy
 * Except the Grid in TRON: Legacy is explicitly NOT the same as that in TRON 2.0 since it's a different continuity, and water in Legacy's Grid acts like, well, water since Flynn programmed his grid to resemble a world more. The programs are not drawing power during the rain scene, for example.
 * I have the feeling that helmet is also a life-support system à la Darth Vader (who Tron appears to be an expy of: see Vader Breath, The Faceless, More Than Mind Control...); thus he shouldn't have any problems breathing "underwater".
 * Of course he is alive. He has Plot Armor; the series is named after him!
 * If that wasn't a Sequel Hook, I'll eat my hat.

Everyone Is Jesus in Purgatory
Kevin Flynn is the white-bearded god, Clu is Lucifer, Sam is Jesus, and Quorra is us, waiting to be saved.

Castor/Zuse is Sander Cohen's program.
Audiences could just see Castor screaming "Fly away, little moth, fly!" and "Smile! Smile, Quorra!" as he was dancing during the club fight scene.
 * Here's something you could do in your free-time. Take the script from the Fort Frolic level of Bioshock. Change Sander Cohen's, Andrew Ryan's, Atlas' and Jack's names to Castor/Zuse, Clu, Quorra, and Sam respectively. Then, in specific battle against Cohen's army, replace the Splicers with the Black Guard programs and change the music from Tchaikovsky to Daft Punk. It Makes Sense in Context and would make an already awesome level even more awesome.

Castor/Zuse is Excalibur.
He's a completely white, noisy, egotistical, pompous Large Ham with a cane. And he dances at the worst moments. Obviously Excalibur is a constant in multiple universes...or something.

The romance between Sam and Quorra was based on Eureka Seven
You got a slacker turned hero (Renton and Sam Flynn), a girl who is not human (Eureka is a Coralian and Quorra is an ISO program), the father tried to protect the love interest's species (Adroc Thurston and Kevin Flynn) and a villain hellbent on annihilating those who are not part of his race (Dewey Novak with his hatred for Coralians and Clu with his obsession with perfection). Not to mention that the romance focuses on the emotional side of love instead of the physicality of love.

If a sequel gets the greenlight, Quorra will become similar to Nia
Think about it. Even though she's an intelligent Action Girl of Legacy, she still has a naive, child-like personality, especially when it comes to topics surrounding the real world. So when Quorra starts living with Sam, she would find adapting to the real world to be difficult. She would also probably lack knowledge of regular customs and surprise others in the real world with quirky misunderstandings. Doesn't stop Sam from loving her though, hence why he will probably propose to her sometime during the sequel. "Olivia Wilde: I'm so thrilled to play with Quorra in the human world. It would be sort of like Splash.
 * This has been confirmed by Olivia Wilde in an article from MTV..

(referring to the '80s comedy starring Daryl Hannah as a mermaid unleashed in Manhattan)

I want to see her whispering to laptops and hugging toasters.... There's a whole other chapter ahead."


 * Bonus points if Dillenger Jr. corrupts Quorra's ISO nature, resulting in a Face Heel Turn against her will, just after the engagement.

Beck, the protagonist of the upcoming spinoff animated series, is an ISO.
Judging from the synopsis found in the website for Disney XD, Beck is a young, impulsive program who wants to save his friends and his home from Clu. This description is very similar to that of the ISOs on The Grid. Moreover, being an ISO would add further urgency to Beck's mission since Uprising will take place sometime before or during The Great Purge.

The coup wasn't entirely a surprise to Kevin Flynn
When Sam brings up the command history on Kevin's computer, it shows he had recently been editing a file called last_will_and_testament.txt.
 * I didn't notice that, but perhaps, since he's the User of the system, the command history just reflects what he's been doing lately in the Grid. (what was the timestamp on it?) Kevin thinks of himself as a tired old man judging by his first conversation with Quorra, and was at least getting ready for his eventual death.
 * No, the history shows what he did in 1989, just before entering the grid. Kevin:
 * Edited the source code of the program that controls the digitizing laser
 * Compiled and installed the new version of the program
 * Ran a "sanity_check" program, likely to ensure the modifications contained no obvious errors
 * Ran "configure", outputting a text file (perhaps a new set of laser parameters)
 * This is somewhat unusual, because "configure" normally refers to a pre-compilation step. Flynn must just have been using the name for a different stage of the setup process.
 * Examined (or possibly edited) the output file
 * Edited his last will and testament
 * Displayed memory usage statistics
 * Displayed all currently running processes
 * Killed process #2207 with signal 9 (generally SIGKILL, the most immediate and violent way to terminate a process)
 * Killed process #2208 (with the default SIGTERM, which allows the process to execute additional graceful exit code first)
 * Displayed all currently running processes, again
 * Set the modification time of an "ok" file for the laser to the current time
 * Most likely, there was a safety module that would inhibit activation of the laser if any files had mtimes after that of the "ok" file. Thus, touching the "ok" file would be confirming that all settings and code were ready to deploy. If other relevant files were accidentally changed afterward, it would not be possible to accidentally activate the laser without redoing the confirmation.
 * Activated the digitizing laser
 * It's possible he just made sure all his affairs were in order every time he went into the Grid in case he were to die in a freak Lightcycle accident or something.
 * If that's the case why the fuck didn't he tell anyone or leave behind an "in case of emergency" letter?

Even if Clu had gotten out, his army would not be able to do much and would be beaten back before even taking the city.

 * Actually, we have no idea what programs are capable of when they materialize. Plus, Clu doesn't necessarily have to take over the world militarily. All he'd need to do to fuck us over is to connect the digitizing laser or the Grid to the internet and "rectify" it.
 * Well, the phone line in the Arcade is disconnected. He'd have to borrow someone else's.
 * Really, all they'd need to do is send a single person into meatspace and hook that computer up to the Internet. If the MCP from the first movie was preparing to overcome a military program (Air Force?) back then, it could be cake with Clu's new virus. Related: Digitized humans seem to keep their human aspects; if a 'real' Clu could infect others from the real world, or have his army infect others like Abraxas from Evolution, then despite its small size it could easily have become a major threat as it spread zombie-style.
 * The MCP's plan was to 'hit the Pentagon' a week from that time.
 * Of course, the MCP was contemporary to the Pentagon's systems back then. Clu is actually contemporary to computer systems from around the late 80's or early 90's. Especially consider that military programs would be no strangers to the Internet and experienced in cyber warfare, Clu would likely get his ass kicked so hard it would implode before derezzing.
 * Not necessarily. Flynn was established as being his universe's computer-age Tesla; absolutely batshit nuts, but light-years ahead of anyone else in terms of the stuff he was cooking up. There's that throw-away line to Sam that he had the concept for wi-fi back in 1985. However, brilliant as he was, Kevin Flynn was an utter idiot when it came to "consequences," and that's what hanged him. (Dear God, he should have at least told Alan or Lora what he was up to as a fail-safe!) His Grid cooked up the ISOs and some A.I. units that would shred the Turing Test. Ghu knows what else Flynn could have cooked up with all that time.
 * Also, think about these two factors: 1)time moves faster in the Grid/the virtual world, and 2)any program's first language IS computer language. We, as humans, do not have an instinctive grasp of computer language, nor do we have contact with computer programs as direct and fast as the programs themselves. If Clu or one of his cronies got into a computer system, they'd understand it better than any human ever could(unless that human, like Flynn, had actually been inside a system), and they'd have fifty times the time of a human to put changes into it. To use an analogy, for us, talking to a computer program is like an English speaker with a dictionary texting a Japanese speaker letter by letter: to the program, it's slow and cumbersome. Meanwhile, Clu and his cronies could go in and talk to them in their native language or repurpose them faster than any human ever could. Plus, how easy is it for YOU to detect a computer virus? Not very, that's why we have anti-virus programs, right? Well, anti-virus programs don't work unless they're coded to detect specific viruses, they can't detect anything they're not familiar with. Hell, Clu could probably repurpose an anti-virus program into a mega-virus capable of doing the damage of all the viruses it was programmed to eradicate. Any security programmed could easily be turned into the electronic equivalent of a nuke by Clu.

Kevin Flynn died long before TRON: Legacy. "Old Flynn" is another avatar program, just like Clu.
Flynn created it (I'll call him Good!Clu) with more sensible guidelines (and without the mistakes he made with Clu) after the coup, to help him and Quorra against Clu. An earlier attempt of Clu to get to the Real World was stopped by a Heroic Sacrifice by Flynn which didn't involve merging, since...
 * Due to Year Inside, Hour Outside, it's been 1000 years since Flynn first entered the Grid. Either he shouldn't have aged, or he should have aged 1000 years. Good!Clu could have been created when Flynn had aged 20 years in the virtual world.
 * As a User, Flynn follows 'real' time because he's of the Real World. If Flynn entered in '89 and it's now modern-day, he's been in the Grid and aging appropriately for the past twenty-thirty years. Betrayal has him spending plenty of time in both the Grid and the real world; if aging in the Grid happened the way you propose, Flynn would have been showing marked differences in appearance (the comic starts before Sam's birth and continues until soon before Flynn's disappearance) if he aged with the passing of cycles.
 * Good!Clu's identity disc wouldn't have been useful for allowing Evil!Clu and his minions to escape the system though, would it? If that was something specific to Kevin Flynn's disc. Note that Sam Flynn's disc apparently wasn't good enough, or Evil!Clu would have been able to escape 30 minutes into the movie.

Alternately, we're dealing with a Nobody and a Heartless.

 * Hey, Space Paranoids is part of the Kingdom Hearts universe. Nobodies don't have true emotion, just the memories and echoes of their past emotions. This would explain why Good!Flynn was so "zen" and calm, despite all the crap that happened, and why Sam (a strong memory of paternal love) was the trigger. Likewise, Heartless seem to like staying that way and want to overrun whatever world they're in. When a Nobody and a Heartless merge, the results are also catastrophic.

Humans and programs can't actually merge.

 * But two programs can, with the explosive results we see. This is Good!Clu's Heroic Sacrifice.

Dillinger Jr. will be the villain of the sequel
Because you don't just get Cillian Murphy to play the son of the original film's villain and only have him for ONE SCENE! It's gotta be setup. Dillinger Jr and his program vs Sam, Quorra, Tron and maybe Flynn or another program based on Flynn.
 * Obviously, Dillinger Jr is going to try and sabotage Sam's efforts and take the company himself due to the blood feud started when his own father was overthrown by Kevin. Bonus points if he's being "encouraged" by Dillinger Sr.
 * The seeds for this are actually a sequel hook aside from the ones at the end of the film. Flynn/EncomOS 12 has just recently achieved Complete. Global. Saturation. It is also the "most secure OS ever", thanks to Dillinger's work on it. Dillinger presumably has access to his father's files, and while the system eventually rebelled because AI Is a Crapshoot, the MCP was a very secure system. Given TRON: Legacy used its budget to revamp just about everything from the old films in glorious new shininess, the sequel has a perfect excuse to both link the Grid to the Web (to combat the resurgent MCP, lying hidden in EOS12), and to bring back both the MCP and Sark, as Dillinger Sr. created the original Sark and would thus be able to recreate him like Flynn did Clu. This ironically would add a bit of Nice Job Breaking It, Hero to Sam's initial prank on Encom in the prologue, as distributing EOS12 for free to everyone ensured that it (and the MCP) would spread worldwide. Assuming other WMGs are accurate (and Disney can get Jeff Bridges back for another film), it's entirely possible that a dream-team of Sam, Flynn, Quorra, Tron, and Clu 3.0 could be the Five-Man Band set to take down the return of their old nemesis.
 * Holy crap, does this theory ever rule.
 * Except most Grids are connected to the web. Every computer has a Grid in it. However, given that the civilian internet at the time of TRON wasn't anything to speak of, the MCP attempting to take it over would be an interesting plot, as well as an excuse to show how the Web is represented in Grid form.

Kevin Flynn isn't dead.
In the excerpt from Digital Frontier on the Flynn Frontier site, one of the sentences is "the easiest way to fix a problem is by restarting," followed by Flynn's agreement. Clu and the altered Grid had definitely fallen into the definition of "a problem," and chances are likely that Flynn assumed he'd die as a result of neutralizing Clu; however, as the ISOs established, even the Creator doesn't know everything about the Grid. Flynn's User-ness will neutralize Clu, yes, but Flynn himself - as the God of the Grid, and a User - will remain. What follows will be a reboot of the Grid itself, complete with restoring from backup the various programs, including an earlier, pre-Rinzler version of Tron. The ISOs, though, may be gone for good, since as spontaneous programs I'm not sure they'd have backups/"original" templates to restore from.
 * It's indicated that the discs contain a complete copy of a program's capabilities and memories. This seems to apply to humans on the grid as well; Clu reviews Sam's pre-Grid memories. Since Sam escaped the Grid with his dad's disc, he essentially has a backup copy of his father. That may be what he copied to the memory card at the end.
 * Sam Flynn to someone at Encom who's about to pop that memory card into their digital camera: "Oh hey, please don't use that one. You might accidentally delete something, and it has my father's soul on it."

The ISOs will come back.
It's possible that, since the ISOs seemingly appeared out of nothing, that more of them may appear on the Grid at some point. The sequel could possibly even be about Sam and Quorra's efforts to recreate them based on Quorra's own ISO code. The ISOs are one of the most unique parts of the TRON lore and they seem too important to just leave without exploring their possibilities.

CLU has all of Flynn's memories and emotions
It could be that CLU has all of Flynn's memories up until the point of his creation. As Flynn said in the beginning of the film, he's basically a copy of Flynn created to look after the Grid while he's away and do everything he would have done if he'd been there. This is why he's so keen to murder Sam instead of using him as, say, a hostage, or putting a tracking device on him and letting him "escape" - he does in fact feel some sort of love for Sam and doesn't like it, so he decides to kill him in the games and get all those messy feelings out of the way.
 * He may have all of Flynn's memories, but it's unlikely that he just wants to kill Sam to get those messy feelings out of the way. He didn't even know Sam had entered the Grid until he showed up in the disc battle arena. The light cycle game was just a public announcement to bait whatever of Flynn's agents are witness (in this case, Quorra) that Sam's on the grid now ("It wasn't meant for them"). It's a Batman Gambit to get Sam and Flynn together to goad Flynn back onto the grid so he can get a chance to snatch Flynn's identity disk.
 * Word of God might actually support this. Lisberger actually went on record in saying that Programs retain at least some memories and emotional impressions from their Users. He even told Cindy Morgan that Yori actually has some memories of Lora's relationship with Flynn. Clu, set up to be Flynn's avatar on the Grid, would likely have even more than that. This may also be why Flynn failed to see Clu had gone off the rails until it was way too late; he assumed Clu had his sense of ethics and shared his love of the Grid.

Clu's plan for world domination is just a distraction
Clu has all of Flynn's memories and understands what it means to be out in the real world. This is supported by the fact that he isn't confused by what he sees when he views Sam's memories and even "expected more", which indicates that Clu himself was able to imagine the real world conditions which would lead to Sam being more accomplished (and even be able to formulate an idea of what is successful in the real world vs. unsuccessful). Clu should have realized that "perfecting" the real world is a nonsensical and stupid idea. Apparently Flynn's vision of perfection within a computer system when he made Clu was homogeneity, but there's no way Flynn's idea of a perfect world was the same, unless he was a secret white supremacist or something (unlikely). Clu may have been perfectly earnest in his attempts to create a perfect system, but by the time he's supposedly plotting to take over the world what Clu really wants is just to escape to the real world all by himself. He got bored of being the boss (and the Grid is pretty dismal when you think of it - always night time, no plants or animals, everything is the same) and now he just wants to go "back" to being a human in the real world (which he would remember being, if he had all of Flynn's memories). In fact, he's stopped thinking of anything in the grid as being "real", which is why he has such a callous disregard for the lives of other programs. He flips out at Kevin's house while looking at his reflection and remembering how he was created because it reminds him that he's not "real" himself. However, he can't go back unless he has Kevin's disk. All the mayhem he was making was to give Kevin the impetus to go somewhere where Clu could steal his disk. He had to give that stupid speech to his stupid brainwashed army so that none of his freer-thinking goons would catch on that Clu was only out for himself. In fact, he wanted Kevin's disk to be stolen back temporarily so that he could get it all by himself without seeming suspicious.

Kevin Flynn and Clu have a symbiotic relationship
The death of one would cause the death of another, which is why Clu doesn't kill Flynn on the walkway, and they can feel each other's emotions which is why Flynn's resistance only make's Clu's program stronger and why Flynn has taken to meditation and other such activities.

Clu is a split personality of Kevin Flynn, not a program proper.
Zen!Kevin is the superego and Clu is the id. .

The Light-Jets stall because their programming is derived from/based on flight simulator plane data.
Not as character-centric as the other WMGs here so far, but after a heated debate with friends where this was the main complaint, this troper finally thought of an explanation. Light-jets are rather similar to light-cycles, except they fly. Flynn programmed them, if I recall correctly (which I may not as it's been ages since I've seen the original Tron), the light-cycles came from a video game that Flynn made. So, when time came to make light-jets, Flynn just took the appropriate bits from the light-cycles and the appropriate bits from another video game, a flight simulator, to make a base for the programming, then built them from there. After all, if code for something already exists...but this would explain why they stall and behave like actual planes in a world with decidedly different physics: they're still programmed to react to atmosphere and gravity realistically because the planes in the simulator that parts of their data came from were programmed to do that same.

The significance of the name Rinzler is... ?
I got nothing. Anybody have any ideas or know of anything? I'm not sure if it's a valid use of the WMG page to solicit guesses, but it's worth a shot.
 * Easy! Do it in the style of loony conspiracy theorists making wild claims based on thin associations of words and symbols. Let's see, the first syllable of "Rinzler" sounds like "rinse," which is an action related to "washing," which is the second part of "brainwashing," which Tron was subjected to to turn him into Rinzler!
 * "Rinz" sounds like "Rez", as in "De-Rezzed", which is what Tron/Rinzler does to his opponents in the games. Clu dubbed him "'Rezzer", which eventually morphed into "Rinzler".
 * Simpler: Clu just used a name that didn't sound like "Tron" after he repurposed him.
 * Alternatively, "Rinzler" was the name of the derezzed Blackguard whose disc Tron took.
 * There's a news article out there that explains the name (I think it may be on io9, but I can't remember). Basically, the writers were looking for an alias that didn't sound anything like Tron. After thinking about it for awhile, one of the writers saw the name Rinzler on a "Making of Star Wars" book on his coffee table (Rinzler was the author's last name I believe) and it stuck.
 * Correct.
 * According to this fanart (pic is SFW, but site is not), it's an acronym for "Remote Integrated Neural Zip Linked Enemy Redactor," which... actually makes quite a bit of sense. Also, acronyms-as-names seem to be popular in the Grid (CLU, MCP, etc.)

Kevin's disc was necessary to use the Portal because he had Root privileges.
Clu, only having Admin privileges, could not access the Portal, and Sam only has User Privileges.

Sending the carrier through the Portal would have resulted in disaster, assuming it was able to go through at all.
The carrier and its occupants would have rematerialized in the basement of Flynn's Arcade, which was not big enough for them to fit. Possibly, they wouldn't have rematerialized at all, either being kicked back or being stuck in limbo. Of course, Clu doesn't know this because he has never seen the other side of the Portal. He is assuming that there's another portal in the middle of nowhere on Earth too.

Scott Pilgrim vs. the World takes place in the TRON universe.
Specifically, the movie takes place inside the game based on the books. Ramona is a User, obviously.

Rinzler's real identity
He is obviously a Timelord a Cylon The Stig.

Think about it.
 * Some say that one of his data streams are longer than the other.
 * Some say that he thought System Shock was a documentary.
 * Some say that he's the one who started the war between pig and bird, and that he's the reason Pac-Man became a Ms.

Flynn was planning on taking Sam into the Grid to meet Quorra the next day, before he was trapped there.
Flynn tosses a coin to Sam, suggesting the next day they go to the arcade to play a few rounds. Flynn was really going to take Sam through the fake door behind the TRON stand-alone and into the Grid, as he promised to do. But why take Sam when Flynn hadn't invited Alan, his closest confidant? Flynn had been raving to Alan a few days before that something miraculous was happening (the discovery of the ISOs, obviously), but why didn't Flynn take Alan to see? Because the real miracle going on with the ISOs was that they could "create" their own programs outside of Flynn's programming: namely, they could mate and have children. And Quorra was the first child born of the Grid. Flynn had probably calculated that by the next day (due to the time dilation effects) Quorra and Sam would be about the same age...
 * It would also explain Clu's behavior: that the ISOs could create programs where he couldn't (he could only derezz or "rectify"), mimicking Satan's hatred of Humanity when God shifted His love to them.
 * If the Isos could reproduce, it could also explain the Fantastic Racism that lead to their genocide; to a Program, it would make them akin to viruses or gridbugs - threats that would overwhelm and crowd out to Programs with sheer numbers, the way some racists today shriek about how the "wrong" people are outbreeding the "right" people. It would also explain partly why Flynn Sr. was so delighted by them; at the time they came out of the Sea, he was excitedly preparing for fatherhood.
 * Given the timeflow difference between the two realms, how could he take anyone to the Grid? In the real world, the person is zapped. In the Grid about 8 hours passes before the beam shuts down and access closes. Back in the real world, it's only open for a few microseconds. The first person in would reappear in the real world before the second one could even start to sit down in front of the beam.
 * I thought the "8 hours" referred to real-world time, or 13 days 6 hours of Grid time.
 * Kevin did state that the beam was only open a few microseconds real-time.
 * The portal can be keyed to remain open longer if Kevin wants it to be. In Betrayal Kevin assembles a device to notify him while he's in the Grid if his wife is about to deliver her baby. He wouldn't need this unless he was going to spend a prolonged period in the Grid in terms of "fleshy" time.

Flynn was only alive because the computer was shut down.
A LOT more time passes on the grid than outside, right? Flynn should have died of old age long before Sam arrived. The solution? Shutting down the system puts the grid and everyone in it into suspended animation. Sam turns the computer back on and the grid resumes as if nothing happened. "Sam: Hi dad. Long time no see...
 * The impression I got was that Flynn aged in real time.

Kevin: *chuckles* You have no idea..."


 * This one is disproved by the run-time clock on the terminal screen, it's display reading 20 years, 11 months, 20 days, 16 hours, 22 minutes, 16 seconds, and 34 hundredths of a second right as Sam wipes the dust off (thanks YouTube!).

Most programs are not intelligent, except for the ISOs.
This is something that was at least strongly hinted in the original Tron, but seems weaker in this movie. When a person is digitized, they see things in a way which is made comprehensible to their minds, which includes seeing the programs as people and their actions as people's actions. The programs are not actually intelligent any more than they actually look like people.

Another related possibility is that they are shown that way for sake of the audience. It's similar to movies with talking animals. We're not supposed to imagine that animals really are sentient with the full implications of that--it's not slavery to keep chickens or murder to swat bugs, even in A Bug's Life. It's just a way of letting us relate to the characters. Likewise, these are just computer programs.


 * The first movie's novel and the supplemental comic books appear to Joss this one. The Programs interact, form opinions, and have a functional (albeit somewhat odd) society of their own. Master Control was also plenty intelligent, including knowing how to blackmail Dillinger into keeping his mouth shut regarding the MCP's plan to Take Over the World and tricking Flynn into letting down his guard long enough to get him zapped.

The Programs are Homunculi, created by digital means, and powered by a spark from their User's soul.
There's a great little scene in the first flick where Walter Gibbs (Encom's founder) is chewing out Dillinger, and part of his rant is that "Our spirit remains in every program we create for this system!" Flynn goes down the digital rabbit hole and finds doppelgangers of the people he knows who are oddly similar to them, and yet developed in an entirely different direction. This mixed with Word of God saying that Programs retain emotional impressions and personality traits from their User...and it looks like what Gibbs said metaphorically is actually quite literal. This is also why Flynn had to sadly admit to his son that "[Clu] is me."

If Quorra re-enters the Grid, she will become something greater than either a User or an ISO.
She's been rendered unto a human once she entered the real world. If she were to re-enter the Grid, she'd still be naively brilliant, as ISOs are, but now augmented by the powers of a User.
 * Not necessarily. Users don't become digital on the grid (they are still human and bleed when cut, not disintegrate.) You don't see Quorra do anything in the real world except ride a motorcycle. She could still be digital.

The essential problem is that Clu doesn't smoke nearly as much pot as Flynn did in the eighties.

 * Clu began as a digital copy of Flynn, who, while flippant and immature, wasn't evil. Somehow, though, his personality manifested as far more aggressive, assertive, obsessive, proactive, driven, etc.
 * Kevin clearly is doing some Abiding in the time he's stuck on the grid, and has turned into a chilled-out zen master in the same time that Clu has not really changed at all and/or gotten crazier. "Knocking on the sky and listening to the sound?" Is that what we're calling it, Disney?
 * If there is an exploitable Ballmer Peak for alcohol, you can bet marijuana has one too, and Flynn is riding it.
 * Does anyone remember the scene in Talladega Nights where it is revealed that the mantra passed down from the protagonist's father that he's lived by and has ended up really messing his life up with doesn't even mean anything to the father and was bestowed as a directive when the dad was really baked? Clu and his need to create the perfect system takes this to the extreme.

Encom is an Expy of Apple.

 * Unix-like operating system? Check.
 * Operating system called "OS" followed by a numeral? Check.
 * Prominent touch screen technology? Check.
 * Employees using Apple computers (in the first movie)? Check.
 * Which all makes the thinly-veiled Take That at Microsoft in the film deliciously ironic.
 * Not to mention, Clu flashes back/freaks out while gazing into a glass apple...
 * ... Would that make Daft Punk's characters iTunes?

Zuse and Gem escaped the End of Line club before it exploded.
We never actually see them derezz, and by the time the place explodes, Clu and company are already a fair ways away from the place. Zuse also "plays all the angles" and couldn't have possibly dismissed the likelihood that Clu would backstab him for it.
 * He does look pretty shocked and horrified when Clu's guys start setting bombs... but then again, Castor could have just been acting shocked so that Clu wouldn't suspect anything. As soon as Clu and company were out the door, Castor and Gem split. And entertaining the theory that Castor knew Clu could betray him, he could have set up some sort of secret escape route or something.
 * Also, he brags to Sam about how how had the stairs to his private office constructed. Seems reasonable he'd have some other self-serving adaptions as well. (And why pass up the chance to see Beau Garrett in skin-tight white latex again?)
 * I predict that Zuse and/or Gem not only survived, but will return in the third movie, having made a Heel Face Turn because of Clu's betrayal.

The FLYNN'S arcade sign was a clue that Flynn survived
While its been obviously not used since the 80's, it may be symbolic that the S is flickering, Sam is the last FLYNN left...The S struggling to stay on could allude to Flynn equally trying to struggle back to life inside the Grid... so once again, there would be Flynns.

Sam's mother was a program
Specifically one created by Flynn himself. He managed to materialize her in the real world which is why Kevin knew it could be done. It's also possible that Sam himself was conceived in the computer world (an early version of The Grid Kevin was working on) and born in the "real" world.

Alan knew the whole time exactly where Kevin Flynn was.
But he didn't know how to get there. It's possible that after his disappearance the publicly-knows digitizing laser lab was shut down and its equipment scrapped or re-purposed. Alan didn't know about Kevin's secret lab but knew of his work on The Grid and probably learned of Kevin's original adventures in the Encom 1 Grid after he returned. He may have even helped re-write Tron to help Kevin and be his own avatar on the Grid the same was Clu was Kevin's. As to why he sent Sam to the arcade rather than going himself it's because he's simply too old. When he got the page from the arcade he figured out that Kevin must have had a secret lab hidden away and was trapped on the Grid calling for help. He sent Sam because he had a better chance of not only understanding the equipment, but also getting his father out.
 * If you want to go with the idea that the events of Tron 2.0 aren't completely thrown into Canon Discontinuity, then Alan's seen Cyberspace and knows how insanely dangerous it is.

Tron is related to Protoman.exe
Or, more specifically The Protomen's interpretation of the digital consciousness of a fallen hero.

Tron 2.0 is not as far into Canon Discontinuity as it initially appears.
Mostly going here because the idea of a Sam-Jet-Quorra Power Trio is just too good not to imagine. However...

Think on it: If F-Con did their homework, they might have figured Flynn was onto something after Digital Frontier was published. Even better, Word of God from Monolith states that F-Con's CEO is Dillinger Sr., who already knew about Master Control's sentience and plans. The Ghost In The Machine comic (written in 2003) also says Flynn mysteriously vanished after a few years back in the analog world. In the game itself, Tron's gone Chekhov MIA -- retiring after Master Control's defeat with no one in any system knowing where he vanished to. Better, Alan's slated upgrade to his program was suspended in 1984, on Flynn's orders. In the game, it's never stated why, but if you go with the Legacy canon, it would have been right about the point where the Grid was being constructed.

In Tron 2.0's Backstory, Master Control ran the digitizer. When it was destroyed, Encom was forced to rebuild the laser algorithms from scratch. However, Flynn's pattern was likely stored, meaning he was the only one who could get in and out. So, quietly, he appropriates one of the backup lasers (you never have one of an expensive experiment like that) and uses it to experiment on his own. This would also help explain why he didn't tell anyone - without those algorithms, no one could follow him safely.

Sometime between Flynn's vanishing act and the events of 2.0, F-Con (Dillinger Sr.) acquired a lot of what should have been proprietary information about the laser. Did Flynn's "in case I vanish" notes and letter get stolen as an act of corporate espionage? Worse, you need to have access to a phone line to contact a pager. So, where did Clu score a modem? There are also the matters of Datawraiths and F-Con personnel (Crown, Popoff, and Baza) who were never retrieved from the system. Did Clu have some "friends on the other side?"

Lora also got Put on a Bus to Washington DC, but we have no idea what happened after that, and she's conspicuously absent in Legacy-verse. Perhaps she did try to replicate the digitizer with the fatal results seen in 2.0 (or maybe a less-fatal, but still damaging, result)? And if you did some Canon Welding with the two, it's entirely possible that Alan started putting a lot more time and effort into Roy's "under the table" effort after seeing cyberspace for himself...

A successful TRON franchise will start a Fashion Movement
It will get that distinctive look out there and some people will jump on it.

Edward Dillinger is not the son of Ed Dillinger; he is the son of the MCP
The MCP actually placed a backup of itself in the real world during the events of the original movie. The rules for returning to the real world in the sequel don't seem to apply in the original system (especially since Flynn didn't have his disc at the end, it fell off his back when he got knocked off the bridge of the Solar Sailer). Therefore there's nothing saying that the MCP couldn't have popped into the world at any time he wanted once the digitizing laser was built. This is backed up by the fact that the voice of Dillinger's father in the Flynn Lives segments sounds like the MCP and not Ed Dillinger/Sark. (and yes, I am aware they were both voiced by David Warner)

The Grid has a limited number of models for programs
When Sam fights a guy in Disk Wars and says "I have a three-inch version of you on my shelf" it's not the same program, just one who looks the same.
 * Sam was joking. He sees a guy that looks just like the toy he had as a child, and jokes that he has a three-inch version of him on his shelf. He wasn't meaning an exact copy.

1980's Encom was run by Mages

 * Walter Gibbs was a Son of Ether, the tradition of Mad Science. He founded the company as a front to find and Awaken others with the game gifts. Inventing the laser was just another experiment to that end. He was just on the verge of awakening Lora by trying to get her to question reality. ("Here goes something, here comes nothing.") Unfortunately, he was so busy with that aspect of his mission that he let Ed Dillinger, an agent of the Technocracy, infiltrate and try to shut down his experiments. The Technocracy often uses the same magic they're ostensibly trying to stop, hence why Dillinger's avatars in Cyberspace were trying to get the Programs to not believe in their creators. Flynn had the potential to be the most powerful Virtual Adept in existence if he were allowed to awaken. Hence why Dillinger had to resort to stealing Flynn's work, getting him fired, and then having the MCP attempt killing him. He just hadn't counted on two things - Alan Bradley being an awakening Virtual Adept in his own right (both his security Program and the Holy Hand Grenade of a Deadly Disc he uploaded), and that the trip into Cyberspace backfired spectacularly. Gibbs was finally able to step away and entrust the real mission of Encom with what was now the most powerful Virtual Adept ever.

Ed Dillinger Sr has discovered the grid.
Chew on this: A lot of people are debating who Ed Jr. is talking to in the bonus feature of the Tron Blu-Ray. He calls him Dad, but the voice sounds identical to the Master Control Program, not to mention it says End Of Line. Well, my theory is that at some point after the first film, Ed Sr. discovered exactly how Flynn exposed him. He found out how to get onto the grid and decided to take advantage of it. Seeing how the MCP almost became powerful enough to take over the Pentagon and the Kremlin, if Dillinger were to discover the grid, this same power would probably be what he would go after, with his main goal to get Encom back (but just like the original MCP, he will probably eventually try to take over more) so this theory says that Dillinger has entered the grid, and stayed there so he could evolve himself into a new MCP, with his son playing the same role that Ed Sr. played to the original Master Control. (My only guess as to why he hasn't taken over the Pentagon yet is that either he doesn't have enough power because he doesn't have as much knowledge of the grid, or he did all this within the last year.)

Sam and Quorra don't really love each other that way.
As others have said, the movie portrays their relationship from more of an emotional angle than a physical one (they never even kiss!). There's also a scene where Sam and Quorra talk about how they both like Jules Verne, along with other evidence that Flynn has essentially been raising Quorra to be Sam's Distaff Counterpart. It would be like finding your half-sibling after your father left and started another family. Thus, any relationship between Sam and Quorra beyond a familial one would probably get very squicky, very fast.

Clu made a deal with Rumpelstiltskin somehow to get control of the Grid. And/Or the Grid is affected by the same curse as Storybrooke
Once Upon a Time has been established to be in the same universe, judging from Henry's game of choice being Space Paranoids, and carting around a Tron lunchbox. Jefferson's Hat would be as good as a laser for traveling between worlds. And the timeline of Storybrooke's withdrawal to the "real" world matches up with Clu's creation date. Say Rumpelstiltskin was able to get a hold of the hat and travel there, or maybe send the White Rabbit through in order to set up shop as Zues and make deals on his behalf. In the process, he starts cutting deals. Clu wants out. He wants to make everything "perfect," but everything comes with a price. The price? Flynn's son...Rumple always did have a thing for first born children.

Clu isn't the one who sent the message...
Zuse was. When Sam Flynn bled at the hands of Rinzler, Clu was as surprised as everyone else that he bled rather than shed voxels, but "Castor" seemed to know him almost on sight despite his physical appearance being so generic aside from his face.