I've been toying with the same idea. Here's what I'd do.
- Free minds can make a Concentration check to speed up their perceptions. This will let them Take 20 on attack rolls or acrobatic skill checks. I know the same effect could be had with Action Dice or somesuch, but I really love the idea of 'make a check so I can slow down the camera and do cool ninja stuff'
- A feat available to download one new skill on the fly. Note that Trinity is the only one we see doing this in the movie, so its reasonable that this isn't something just anyone can do. Only one at a time, and lasts until you unplug.
- Compter Use for the Operator to do such things as find exit points, find entrance points approximately where you need them, and send people in with gear. (weapons, vehicles, etc)
- After a lengthy arguement on RPGnet, I would not give the Agents ungodly dodge ability to reflect them dodging bullets. Rather the Matrix itself has a rule that 'if an agent is about to be hit with a projectile weapon, move the agent out of the way.' Otherwise you get into arguements about 'well why can Neo punch an agent but not shoot him' and 'how come Smith didn't dodge the train'.
- Does it have anything to do with my muscles? In this place? -- redo the stats while in the Matrix. Int = Str, Wis = Dex, Cha = Con. Only the mind matters, not the body.
- Style Counts. Perhaps a feat or talent that allows a free mind to deck themselves out in a distinctive look. This gives them a bonus to their Charisma (and thus their Con). However, maybe on a crit part of the outfit is damage, losing the bonus. You know someone is in trouble in the Matrix when their sunglasses get broken.
HTH
