Well this is odd idea.
Each time a System is damaged, a card (top most likely) of the opponent's deck is placed under that card to note how much damage it has taken. Simply so to avoid needing to bring any unnecessary item's to the game other than your cards. If a System is fixed (re-activated) those "Infected" cards go to the discard pile.
Also Dabem, I saw you suggesting life variables? Do you mean both players have various System Cards that = a Total X (say 9) amount and it's split in different ways, like you have 3 systems with a value of 3 each and your opponent has 2 systems, one at a value of 6 and the other at 3.
Or do you mean closer to WoW? Where the HP total is different depending on the Hero used.
As another idea (inspired by the WoW thought) what if Players use just 1 System Card? And the effects they would be allowed to use de-activating the System cards of the older rules is rather gained progressively, so on 1 Damage to system, you can activate an okay effect. Then once you reach 3 damage, you can do something even cooler and then when you reach like 9, even something more insane!?
Also here's a great kicker idea to that, the activation cost of this progressive effects, is reducing the damage down to the level of the previous effect? Essentially, your trading Tempo Damage-wise for Tempo Card-Vantage wise?