Listen you guys, Marcus is ridiculously B.A. dude. He's got the chainsaw, the soul patch, the bandana, the voice that sounds like two boulders mating, he's the second face of the Xbox 360 Mount Rushmore, right next to Commander Shepard, the Hero of Bower Lake, and THE MASTER CHIEF. (if someone can photoshop the above described image, I will worship you as though you were a god)
But when it comes to fighting, The Master Chief simply has him beat down. Yes we can see Marcus' muscles are huge, but have you seen that trailer for Reach, where the young soldier gets injected with a serum, then rises up because of the massive amount of muscle mass gained? That's for a Spartan-III. (Heavy-duty Halo lore ahead) Spartan-III's are the "cheaper", "easier to make" Spartan soldiers in the Halo Universe. The process of making them becomes ridiculously easier after the first successful Spartan-II experiment, but this increased cheapness and quicker production put a hamper on their prowess. In other words, If a Spartan-III is a pro-football player in terms of muscle, then a Spartan-II is a world-class Strongman.
The video here depicts the "Making of" a Spartan-III. Note the body mass. Now consider how much more powerful a Spartan-II is. And The Master Chief isn't just called "The Master Chief" for shizzle's and giggles, he was once just referred to as "John-117". He was the BADDEST OF THE BAD, the ultimate Spartan-II. According to Eric Nylund's Halo-Universe novel, The Fall of Reach, The Master Chief was able to take down four of the best ODST's the UNSC had in service. That's four of THESE guys, the NIGHT AFTER he received the Spartan serum. He was SIXTEEN.
So in CQC, The Master Chief would probably be able to rip apart Marcus Fenix's Badassness. Let's not forget size here as well, Marcus is I'm guessing a good Six-footer. The Master Chief is SEVEN AND A HALF feet tall.
The question of armor also comes into play, and I see many posts stating that The Master Chief has little armor. Ahem. In the first Halo, the MJOLNIR Mark V armor has self-recharging shields that are easily taken down by PLASMA, and have a strong resistance to BALLISTIC FIREARMS. Guess who has only ballistic firearms and no shields? Marcus Fenix.
The armor gets even more powerful in Halo 2 and 3, where MJOLNIR gets an upgrade, and Mark VI armor makes an appearance. Not only do the shields recharge, but the suit repairs the FLESH OF THE WEARER.
Also, the MJOLNIR armor covers more of Master Cheif's body than Marcus' COG armor.
Firepower is pretty similar in these two cases. The humans in the Halo-verse haven't really gotten too far past ballistic weapons, and while it appears as if Sera's humans have increased the caliber-size of their guns, a ballistic weapon is a ballistic weapon.
However, there are a few variations. Yes the COGS have the Hammer of Dawn, but its a very... "Outdoorsy" weapon in the most literal of terms. It can't go through buildings (as I've seen) and if The Chief takes the fight indoors, the two combatants would be on the same playing field in terms of basic ballistic weapons. The Chief, however, has a few 2552 weapons to pull out his butt. First off, the Spartan Laser. It's essentially a portable Hammer of Dawn that shoots HORIZONTALLY. Yea it takes a bit too charge, but it has incredible blast-back power and can knock some pretty large debris Marcus' way. The Chief also has a wider variety of "accurate" weapons to choose from than Marcus. Yes Marcus has the Torque Bow and the Bolt Rifle, but the Chief has the DMR, Battle Rifle, scoped pistol, and a longer-range sniper rifle of his own. Shotguns however, Marcus wins out. That thing is INCREDIBLY OP, and fun. Oh how fun it is...
We also have to consider their minds. In the simplest of manners, let's just pull rank right now and get it over with. SERGEANT Marcus Fenis versus THE MASTER CHIEF OF SPARTANS, John-117. But that's just taking things on the outer level, let us dig deeper.
The Master Chief is ridiculously experienced and ridiculously smart, otherwise he wouldn't be deemed the MASTER CHIEF OF ALL SPARTANS. Marcus Fenix is indeed experienced, but the kind of high-stakes missions Marcus takes are totally different from the missions Master Chief takes.
Let us elaborate, Marcus goes on missions against a terrestrial threat that uses the ground to its advantage and is on a pretty even level TECHNOLOGY WISE with the humans of Sera, only their various species and unpredictable attack strategies give them the massive edge. The Master Chief is sent against the massive forces of an Imperialistic Galactic Religious Hegemony of various multi-planetary species that are equipped with technology left behind from the most powerful race to wander The Milky Race, a race that was able to find EVERY FORM OF LIFE, perform a "Noah's Ark" cleanse, and then REPOPULATE THE GALAXY before departing the Milky Way.
So who takes on the harder challenges? Granted, this isn't calling into question if Marcus is a wuss or not, the Locust are indeed a formidable foe, and Marcus has shown many a victory against them, but The Covenant are simply the more powerful villain, requiring a more powerful hero to succeed in battle against them.
My closing words are much like my opening ones. I am NOT saying that Marcus Fenix is a wuss, quite the opposite actually. Marcus Fenix and the rest of Delta Squad did to the Xbox 360 in 2006 that The Master Chief did to the original Xbox in 2001, gave the populace a reason to buy the console and enjoy the various exploits of the awesome characters. Again, they share a space on the Xbox 360 Mount Rushmore, but if it came down to a one-on-one battle between the two of them, the more experienced, stronger, smarter, faster, and better equipped of them will win out. Again, names. He's not called "The Master Chief" because he won the Name Lottery, John-117 had to EARN that title. He's not just a Super Soldier like the other Spartan-II's, he's a future-day Beowulf, taking the victories and glories in like its nothing and thinking nothing of his actions, thinking only about what has to be done and the reason for him doing it is greater than his wants to not do it.
-Chillz