Welcome to another pointless battle royale thread! This episode, we deal with two heroes whose claim to fame is surviving the most inhospitable of places: apocalyptic disaster zones. These gents have shown they have what it takes to stay alive, no matter what it takes... but if the wastes won't kill them, then a duel to the death surely will!
In this corner, we have:
The Vault Dweller of Fallout fame.
A young fellow who left his home in Vault 13 to seek out a water chip, he quickly became one of the most influential figures in the Wastes. Facing down mutants, raiders, and all manner of other horrors leading up to the enigmatic Master himself, the Vault Dweller has come through the worst of circumstances still wearing that goofy '50's grin.
The Vault Dweller could be many things, from a smooth-talking sniper to a pacifistic scientist to a retarded superhuman smashing machine. "He" could even be female. He could be armed with guns, knives, explosives, or his fists, and armored in a super-suit or whatever junk he could find. But, whatever path he takes, there is no doubt that an experienced Vault Dweller can be the absolute best in the world at any one thing, or even any two things... but could the Vault Dweller be crippled by overspecialization?
And in the other corner, we have:
Marked One, AKA S.T.A.L.K.E.R, who won glory in the Shadow of Cherrnobyl.
Marked One is a mysterious figure in many ways. No one knows exactly where he came from or what he's doing, but one thing is for sure; he'll find a way to survive, against any odds. Whether he faces bandits or mutants or hazardous radiation or brain-scorching radiation or the entire freaking Ukrainian Army, he'll still manage to pull through.
Where the Vault Dweller is notable for exceptional talent in one or two things, the Marked One is skilled in many things. An acceptably good marksman with all manner of weapons, a decent paramedic, a passable thief, and a masterful wildnerness-survivor, the S.T.A.L.K.E.R. is equally good at scavenging, trespassing, adventuring, loner-ing, exploring, and robbing. He too could be armed with just about anything, but is somewhat distinct from the Vault Dweller in that he can buy gear from outside of the Zone instead of always having to scavenge or buy what other people scavenge; for this reason, the Marked One is usually better-armed than the Vault Dweller. But are arms alone enough to take out the dude who conquered a mutant horde?
Who will win? You decide!

The oracle has spoken.

Screw the oracle, it's inaccurate anyway given the games are almost exactly a decade apart. Much as I love STALKER, it's Vault Dweller all the way.

The Marked One wins because he doesn't have to wait for his turn to come up. ;)

Simon Belmont!

A Vault Dweller walks slowly towards Marked One. A post apocalyptic sun shines brightly at his blue vault spandex with bright number 13 on the back. He is unarmed besides a small grin on his face.
Stalker does not hesitate. He rises his IL 86, found not long ago on a dead bandit just outside the city limits. Under a second he aims at the Dweller's head and pulls the trigger.
The wasteland peace is disturbed when a loud bang echoes through it. A perfect hit.
Vault Dweller does not even blink. Continues his slow march towards Marked One with unchanging grin on his face.
Stalker is stunned. Yet a normal human wouldn't even notice that. He had been against monsters of the zone and survived so he quickly recovers, aims and shoots again.
Four bursts hit the wasteland traveler directly at his unprotected chest. Every single bullets hits. The noise is tremendous echoing through desolated radioactive wastes.
He doesn't slow down.
Marked One is shocked. All the monsters he fought none could survive the barrage this lone man just had.
Vault Dweller stops two feet away from Stalker looking him directly in the eyes with that small grin he had since the beginning of their encounter.
Slowly he raises his left hand, without haste, without worry. Stalker manages to whisper: "That's impossible"
A powerful blow hits Marked One. It shatters his jaw, breaks the neck flinging the body high in the air. The blood spills on the red sand when the body finally lands with loud thud. What once was Stalkers face covered by gas mask is now nothing more than a grotesque pulp of flesh, blood and plastic.
Vault Dweller chuckles softly and says: "I read the Hintbook, son. You never stood a chance" and walks away towards the setting sun, the champion of Wasteland.

Only if you believe in popularity contests.
Yeah... the way I figure it, the Vault Dweller's famed ability to take fatal or nearly fatal injuries (direct hit with a rocket!) and remain standing more or less cancels out the turn-based combat problem.
In any case, if you assume that both characters are both fully loaded and both operating in either real-time or TB-time, I believe that what really makes a difference is how the Vault Dweller's SPECIAL stats are set up out. I wouldn't give a fig for his chances if he were designed to be a noncombat specialist, or a melee specialist, but the rules change if he's put enough points into ANY of his weapon skills. The effective range of VD's weapons with a maxed-out small guns, big guns, or energy weapons score appears to be a lot higher than the Marked One's. With the right perks, the Vault Dweller's first shot will probably be the last and only one in the fight; if there's one thing the Marked One is NOT known for, it's resistance to headshots.

if the Dweller has Dogmeat its over...

I figure a fair fight has to be one-on-one. Taking on the Vault Dweller would be tough; taking on the Vault Dweller alongside his pals (Dogmeat, Ian, Tycho, Katja, Dogmeat II, K-9, Cyberdog, Vic, Cassidy, Marcus, Sulik, Skynet, and Myron baby, Myron!) would be impossible.

Gonna have to side with Marked One on this. Staying alive in the harsh wilderness of the Pripyat Exclusion Zone around 2010 is a pretty incredbile feat, and the vault dweller has to level up all his abilities since he's always a noob right off the bat.
Plus, Vault Dweller wouldn't be able to find any 10mm ammo.

Vault Dweller needs no ammo. He'll find a way to sleep with the marked one, get him hooked on drugs, and persuade him to kill himself spectacularly, and then read a magazine.

I like to think marked One would win personally. But that is because i like the S.T.A.L.K.E.R. games more. But then The dweller only has to roll to hit, whilst Marked one relies heavely on what gun he has. Kinda hard to say considering the two are from two different genres.
I cant say, i think Marked one is more harcore though, if that is any help. :P

The Vault Dweller, easily. Lukaszthegreat already summed up why.

Vault Dweller wins by coming from the setting with the dodgiest take on reality.

Vault Dweller would win because STALKER would crash before the end of the fight, and his weapons are so inaccurate that he'd never hit anything if it didn't.