Damn. Like a lot of the game suggestions he makes, this one is particularly good. It's original, awesome-sounding, and (unfortunately) was never actually acted upon.
If I could offer suggestions, mostly in regard to the control scheme and perspective thing, why not allow the use of the first person perspective instead of constant second-person? And yeah, normally it's third-person, but I think this would be the first instance of a second-person game.
But, at any rate, the perspective: allow players to view things through their destroyed eyes, but view the ship by its blueprints or floorplans. In other words, the world you see is basically darkness covered by the lines that denote where everything is supposed to be. A wire-frame world, I suppose.
That leaves the monsters, however. They're obviously not a part of the blueprints, and neither would debris, wreckage, etc. That's where the security cameras come into play. When you 'activate' a camera, it adds the camera's field of vision to your perspective. In essence, it takes the slice of the room/hallway that the camera can see and puts it onto the wireframe. You can't view every camera at once, so you need to pick which one you're looking through. As an upgrade to your neural chip, maybe you can 'look' through two at one time, widening the area in any given zone that you can see.
As a backup, and for areas without working cameras, you get a handheld camera. It's not a great camera to begin with, and it didn't fare too well in the chaos, but it can give you a tunnel of vision that sees the world as it is. Think of it as a flashlight for an environment that's still fully lit, yet completely black from where you're standing.
I think that the handheld would be powered by semi-common powercells that can automatically recharge, but only if you don't burn them out. That way, you won't be punished for lingering or exploring provided you pause to let them recharge (or venture forward and rely on the blueprints/security cameras), but there's an element of urgency to using it in an unexplored area that you haven't found cameras for. And, to be generous, you can recharge a dead cell at a designated port of some kind, just so you never get caught having used all the cells in an area and can't continue.
As for the plot twist...that could easily play into the rising difficulty of the game. Early enemies might be survivors or infected, and thus be largely melee-centered or wielding light weapons/light ranged attacks. Later on, suddenly there are enemies who are tougher and stronger, and fighting with the existing ones. And finally, you're up against creatures that dwarf all previous, and it's not so much about 'fighting' them as evading and surviving their presence. The second group is the first-responders to the disaster, and the third group would be whatever paramilitary unit that gets called in when it's clear that the ship can't be reclaimed without force.
So...yeah. I guess that's about it. Oh, and it might be worthwhile if the virus also picked out a small group of people who would see each other as human: it allows for the protagonist to run across fellow humans to reinforce his belief that what he sees is reality, and the effects would be the same on them.
