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).

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.)