This seems like a good idea, but I think you're heading in a direction in which civ won't function like a matrix civ game, but instead like a weird matrix rpg/tbs game. You should really put a lot of thought on how this could go.
I have several thoughts you could use. For one thing, the basic army unit for the rebels in the later ages can be an easily made E.M.P. device, which would be the same as a cruise missile except it would destroy all of the machines units in the tile it hits and in the adjacent squares, kind of like a nuke for machines. The basic machine unit in the later ages could be the sentinel. Also, for the pictures of mines and irrigation for the machines, you could make it be a drilled hole in the ground for mine and the fields of humans for irrigation. Also, I think you should make all of the main characters in the matrix just be leaders, who have an attack and defence instead of just movement points, who could also be used to complete a wonder or build an army. This way, you actually have to wage some war to get Neo, Trinity, Agent Smith, or any other character. Also, I think having the co-existors will be too complicated. Instead, have there be units (programmers/machine's converter thing) that can convert units from the other side. For example, one of your programmers might be able to convert a sentinel. Also, the sentinel could be the basic worker but have an attack as well as movement point. Also, you should see if you can make a tech called "Underground Cities" specifically for the humans, and then, all of the humans cities would be hidden from view from the machines and the machines can only see it by converting one of your workers/non-machine unit. Then just make the transport become the hovercrafts (Nebuchadnezzar/Logos) and make them have no attack but a good defence and if attacked they cannot move the next turn(i.e. emp has shocked all of the energy out of them). There are many more ideas you guys can come up with, you guys just have to sit by a computer for like 2 hours straight and type up the basics first (i.e. Ages, basic units), and then go into the details (how to make the units, and make the units be speciffic to races).
. That's it.
