I'm really not convinced adding another damage track will do anything but make the game slower and more complicated. Babylon 5 space combat is fast and brutal, almost all ships seem to be destroyed in the show by a few devastating shots, so the crit system is good. The problem is that a few stacked crit effects render a big ship pointless, where a smaller one would have died by that point. We also see in the show large ships being repaired of critical damage very fast.
One of our players came up with an idea, what do you think of it? We haven't tested it yet, he just put it out there for discussion, feel free to strawman it.
Bigger ships have more auxilliary crew not involved in the battles (extras to cover shifts, since the best and brightest are manning the actual positions), more spare parts on board, and more back up systems. Because of this they can repair the effects of critical hits more easily. For every priority level above Raid the ship is it may attempt one additional repair roll in the end phase. Thus, Patrol-Raid get one repair roll, Battle level vessels get two, War ships get 3 rolls and Armageddon four. This allows crits to be devastating, but lets big ships get back into the game fast if the enemy doesn't hammer them continuously.