It was pointed out on social media that Jet and Beck have an odd resemblance to one another, not just in appearance, but in personality and even fighting style (not very good in melee combat, very accurate at ranged combat, reliance on parkour and stealth). The rocky relationship between Tron and Beck also resembles the equally troubled relationship between Alan and Jet. This follows one of the oddities from the first film - where the Encom Programs resembled the User who made them.
There are two possible ways it could have happened. Either Kevin Flynn was grooming Jet for The Grid like he was grooming Sam, and did a lot of the heavy lifting in helping a very young Jet code up his first debugger. The other possibility is that Uprising takes place later than expected in the timeline, and that Jet had uploaded a Program to the Grid to assist Tron after the events of the game.
- Fridge Brilliance - think about Jet's inability in-game to kill innocent Programs (with the Heroic BSoD he suffered in the comic over the lives he did have to take) and Beck's reluctance to kill anyone, even an enemy. Secondly, if Jet did code Beck, that might explain a lot as to why he went looking for Tron in the first place. Fridge Horror - Beck's survival odds are quite dim. Consider what that might do to Jet if he finds out his Program was brutally de-rezzed and he wasn't able to prevent it, or Tron's reaction to his apprentice's User.
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 M.I.A. 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 Back Story, 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 cached in the system, 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. Top it off with the lock in the arcade basement. The key in the lock was far too shiny to have been sitting there since 1989; someone else had access. 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, aside from an appearance in the ARG. Maybe the accident mentioned in 2.0 happened, but with 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...
Word of God from Monolith says it's Dillinger Sr., but consider how Dillinger Jr. was contacting his "father" in The Next Day, and the fact that David Warner played both. We never see the F-Con CEO; we just hear him via the PA system and camera movement, as well as see his emails. It's the Terrible Trio doing all the legwork. Say Dillinger Sr. got himself a setup like Lora-Ma3a , where he's a human merged with an AI. And if it is Master Control 2.0, it's Fridge Brilliance as to why Alan was captured - he'd have just as much a grudge against Tron's creator as he would against Flynn!
Assume that Master Control was defeated, but not destroyed. His "take over the virtual and analog worlds" plans had a serious setback. It's not a total loss, though. He's still got piles of embezzled cash from the corporations he took over. He's got access to all kinds of computer networks (which will only increase with the invention of TCP/IP and modern computer networking) plenty of time, and many, many reasons to have a serious grudge against the Flynn/Baines/Bradley Power Trio and any of their Programs. So, he waits, lies low, and gathers strength as computing technology improves. Flynn builds The Grid, and it's almost, but not quite an isolated system (after all, it could still send a signal to Alan's pager). Master Control sees an opportunity, and starts playing Supreme Leader Snoke to Clu's "Kylo Ren", listening to the Administrator's frustrations, being his "friend," making the odd suggestion on what he can do to that careless User and his precious Isos...(Remember, Flynn vanishes in both timelines, making the events of Legacy entirely plausible in 2.0 continuity)
Okay, now Flynn's out of the way, and Tron's not going to be a threat (at least not until after Argon's destroyed), time to turn his attention to Alan and Lora. Arrange for an "accident" in the laser lab to take Lora out of the picture (either death or injury, depending on timeline), and keep Alan isolated in one form or another. And all that embezzled corporate cash and company secrets? Let's start making a company of his own, one speckling in "secure" offsite data storage (all the better for him to go snooping). Hire Crown, Baza, and Popoff to be the fronts there, plant Dillinger Junior and J. D. Thorne as moles inside Encom, and start setting things up for his minions to get Shiva technology and send their army into Cyberspace while Clu gears up to try and invade the analog world. Whichever of them succeeds, Master Control wins and gets revenge. Unfortunately for him, the Spin-Offspring are just a little too good at screwing up well-made plans.
While all digitized humans become incredibly powerful inside cyberspace, and have a "base" set of abilities (higher energy storage, more durability), the rest of their powers can vary wildly and reflect who they are as a person in their own world. Flynn was a consummate manipulator (look how fast he was able to talk both his ex and his ex's fiance into a six-felony night or how loyal they are to him even 20 years after he vanishes!), so his abilities reflected that. He manipulated matter (the Recognizer), energy (draining Sark's Mook, the transport beam), and even pulled a Jedi Mind Trick of sorts on the guard in TRON: Legacy.
In TRON 2.0, Thorne was relatively powerless and frustrated with his life in the human world, and was vulnerable to corruption by F-con, who promised great riches and power. Once he got into the digital one, he instantly indulged both his desire for power and inner corruption by becoming "Master User Thorne," and corrupting a horde of Programs into PlagueZombies. On the flip side of the coin, Jethro Bradley did everything he could to avoid power and his abilities centered on using what was already available (archive bins, downloads), including being able to wield corruption-based weaponry without becoming corrupt himself. The only hint we get about what Alan Bradley may have developed is seen when he is able to analyze the Wraith server's schematics and plot out a plan to take it down from the inside - then again, he wasn't in the system for very long.
In TRON: Legacy, Sam is shown to be adept at breaking and entering, dangerous stunts, and fighting. It's also implied that he's inward-facing as a result of his abandonment issues. It's entirely likely that he was drawing on User abilities in both the Games and in other combat situations, enhancing his strength, speed, reaction time, and subconsciously "reading" his enemies for weaknesses. It also allowed him to get into places he shouldn't have been able to access - like Clu's control room.