Ah, the Matrix. You know, I could represent it with qualities, just like everything else in FTD, but for this I'm going simpler yet. The reason is that this is a realm that's likely to split the party. Never, ever have I seen a group where everyone's equipped to go VR, even with the new accessibility options in Shadowrun 4. This means I want a resolution mechanic that's even faster, so that we can handle the hackers and technomancers and then get them back to the meat world with the rest of the party.
So I'm ripping the mechanics for this straight out of a game called There Is No Spoon, a game designed to model the action of the Matrix movie. It'll require some reskinning, since the meat world of Shadowrun looks a lot like the digital world of the Matrix movies, but the rules are about as simple as they can be, and that's very important.
As to how you get your Matrix scores, that comes off your Runner Type quality. If you've got a Runner Type that's involved with the Matrix, like Hacker or Technomancer, then you get that quality's rank in points to build your Matrix persona. It works well that characters in There Is No Spoon are built on 6 points, since that's the maximum value for a quality. This means it scales perfectly, and yes, I think you could probably make a passable hacker with only 2 points.