We all know that, player skill aside, Isaac is special. He's normally at the centre of events in the Dead Space universe. Hell, even Altman had a prophetic dream about the guy!
But what exactly makes him so special? Is it his ability to destroy Markers? Apparently, Stross would have been perfectly capable of doing this, if he hadn't flipped out and nearly killed Ellie and Isaac. It would seem then, that, logically, any patient would have been able to do this, given they had a strong enough willpower to remain in control of their actions. So why is Isaac so special if we could essentially just home-grow people capable of destroying Markers in the event that Markers must be destroyed?
Here's my idea: It's all simulated.
We know that the Site 12 Marker was allowing the science team working on it to make it to a certain degree, and I believe that the Black Marker is, in its own way, doing this to Isaac.
Think about it. Isaac has little formal military training. He is fighting against creatures with knives for arms with a space-age stapler. On more than one occassion, these creatures have been unkillable unless under special circumstances. Is it really so easy to think that somebody with skills that six out of ten people will have is capable of not only surviving, but also deconstructing a threat that has existed for a couple millenia, and may very well have wiped out a race of people that can make artificial intelligence from a black stone?
So, the Black Marker is almost without a doubt, very, very intelligent, perhaps more so than mankind's greatest minds. Perhaps, then, it is smart enough to simulate all the possible outcomes of a situation, manipulating events through the many people that come in their droves to see the lies spread by EarthGov in action. Perhaps it even influenced the creation of Unitology to provide itself with a willing army, should it need one.
So, simulating these events through its incredible intellect, it could reach a point where having Isaac around would be useful. Say Isaac investigates the original labs in which the Marker is situated. He blasts through hordes of Necromorphs, convinced that the Marker is trying to stop him.
Then, at the last second, it tells him that it can stop all the Necromorphs from coming into being ever again, but only with his help. Isaac, successfully convinced, takes it to a pedastal. All Hell breaks lose, however, as the Necromorphs come back, stronger than ever before, and ready to take the world over to the will of the Marker. Since its dastardly conception, it has influenced events, shielded Isaac from harm, and torn countless lives asunder for the power it will now receive.
Of course, this doesn't mean Isaac will be torn limb from limb at the end of the franchise as the Necromorphs wage a blood genocide on man. I would be very, very pissed if that happened. What I imagine would happen is Isaac destroys the Marker, perhaps dying himself in the process.
Welp, there's the first speculation into the end of the series that (I don't think) has any plot holes.
Think what you will, and thank you for your time.