Hi Sircuri,
I have had a quick look at your documents, and the the first thing I have to say is that I commend your for documenting first then coding later! I should follow that principle myself on a more regular basis.
Most people who are into PC's are gonna dig the Matrix so you have picked a good theme. They will probably have high expectations as they will expect the game to conform to parts of the flim. So NPC, rooms and objects will need to give an impression of scenes that are similar to the film.
I agree with a point that Alex's makes regarding balance you have written the storyline from the perspective of a human, and that is only half the story, as it is the machines that are in charge not the humans. Initially it will be tough to make progress as a human, and I am sure there will be many people that will want to play as andriods/machines in attempt to stop the human making progress. NPC representing both sides that fight and interact with each other would really help set the tone for what the world is about.
I like the idea for the instructor for a human player. That could be a key part of the gameplay for humans.
Sorry for the brief review but if you flesh out the document some more I would be happy to review it again. Perhaps you could add some technical elelemts to the next version of the document relating to the sort of functions the instructor would perfrom.
ie the mainframe may change/extend the use of the weather system system from the stock DS2 mudlib to make announcements to all players.
You could also maybe code an introduction/training element to the game to immerse the players in the world before enetering it for real.
Hope my comments help.
Saquivor