OS = Operating System
GUI = Graphical User Interface (Point and click. Windows)
The operating system the users were using looked like a command line interface. Like, instead of clicking on things, you type in a word, phrase, or string and hit enter. Not unlike the Commadore 64 systems of yore. Sorta looked like BASIC programming language. It makes sense, because with such an OS, the users could only operate one program at a time. Whereas using a GUI, they could multitask. Since everything began with such a command line interface, it's hard to judge which one it is comparable to today.
I'm saying that the MCP took Flynn's entire being, consciousness and all, and converted it to data that could be interpreted by the digital world. *shrugs* It could have also just taken his consciousness and left his physical presence suspended in the beam. Though, in transporter examples such as Star Trek, when someone is transported, their "pattern" gets put into a buffer until it can be reassembled. The pattern is everything. Their mass and consciousness. This beam seems to work much the same way, only instead of holding his pattern in the buffer, it was translated into interactive data.
I believe the MCP ordered a double latte' and got a Flynn soda instead. I wonder how much caffeine a Flynn soda has...