The MCP's control over the computer system is a very loose analogy for Soviet-style communism.
Despite operating within a very capitalist corporate enterprise. To wit:
  • The stated aim of the MCP is to make the system run more effectively for all, much like communism aims to better society. Unfortunately, all it does in practice is to make life difficult for ordinary users whilst the elite benefit.
  • The way the MCP seeks to take over everything is analogous to the idea of the state taking over the means of production, and the fact it's trying to spread itself to become a worldwide movement.
  • In the computer world, the way the MCP "regime" treats the "religion" of the users is somewhat analogous to the way communist regimes have treated Real Life religions: officially oppose them and persecute their followers, but still find you have to keep them around because you can't quite get rid of them.
  • As well as the way dissent is suppressed and there is very little individual freedom for ordinary programs (citizens).
    • Although on second thoughts, whether this is of a level like the Soviet Union so much as maybe North Korea...

The computer world Flynn experiences is, in part, a dream state.
It would be very difficult to see the ordinary programs as being anthropromorphic, let alone representations of their authors, in actuality. Especially running on 1980s technology. So it may be that what Flynn experiences is in fact an attempt by his subconscious mind to cope with his digitized state. Of course, with the MCP being sentient, there's nothing to suppose that the MCP doesn't re-write the code for the programs he has no immediate use for to play videogames for 'his' own amusement.

The Grid seen in TRON: Legacy, based on this theory, would be something based on Flynn's experiences in the first movie, only more real as it runs off much more advanced hardware (created for the purpose in-universe).
  • Lore from production and backstory of Tron Legacy - some of which was used in the Flynn Lives AR game - suggests that Flynn set up the Grid as a place to research advanced technology. He purposefully increased the complexity of its physical simulation so that stuff like Light Cycles could be designed as functional machines. By contrast, the Encom mainframe's computer world from the original film was an accidental creation; Users were not intentionally trying to define reality inside it.

If the MCP had got its way, The Singularity would occur
Seeing it claims it can run everything hundreds to thousands of times better than any human and has essentially achieved sentience in the real world. Who knows what it could be capable of?

(Mind you, it seems it has the all-too-human failings of greed and lust for power, so maybe not.)

Most computer systems aren't filled with living programs
The ENCON system is, for its time, a ridiculously advanced system. They've experimented with things like digitizing, who's to say it wasn't their experiments that caused the programs to come to life?
  • Jury's out on Legacy canon, but definitely Jossed in the Tron 2.0 continuity where Jet travels through multiple computer systems (Encom server, old mainframe, Internet node, even a PDA) , finding sentient Programs at every stop.

User abilities will vary depending on the person's personality and skillset (crossposted to TronLegacy and TRON 2.0)

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.

Related to above, Master Control wasn't destroyed, only defeated. The events of TRON 2.0 and TRON: Legacy were orchestrated as revenge (crossposted to TronTwoPointOh and TRON: Legacy)

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 (being taken down for good sometime 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 specializing 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.