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 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 occurSeeing 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.)