: Captain America, being superhuman, is by definition stronger than John ever
: could have been without augments.

Says who? Keep in mind that without the super soldier serum, Cap would just be a scrawny and weak Steve Rodgers that would be in his 80s or dead at this time. And not taking in time differences (cause we're clearly not with this fight), who's to say john would have grown up to be a soldier and left Reach to fight the Covenant?

: Batman is probably more intelligent and
: better at psychology than Mendez.

You're assuming again. Mendez had far tougher training the Bats did because his career demanded it. A lot of Bruce's training is self taught and through having money to get the lessons he got. Without the money to back him up, Bruce would just be a nutball in costume. He may have taught himself some skills but nothing on the level of Mendez, Halsey, and the numerous AI teachers John had.

: Adamantium cladding beats carbide
: ceramic ossification unless it's Magneto you're fighting against.

That is if you don't have a supercomputer living in your head to wirelessly generate and activate giant magnets from your surroundings. Or drop any heavy object on Logan. Logan has a healing factor and unbreakable bones. But he's not super strong, fast, or very intelligent. Heck, he's not even tall. A simple gaint construction magnet could hold Logan at bay as could any heavy objects that pin him down. John's strength, speed, and intellect could stop Wolverine. Stick him to a magnet and drop him in a vat of melted Adamantium or a valcano and it's game over for the old man. John's to smart to let Wolvie get within arms reach of him. As are Spider-Man, Ironman, Batman, and pretty much any smart hero or villian.

: And Tony
: Stark's suits are probably a lot more versatile than MJOLNIR.

20th-21st centery tech versus 26th centery tech. Hmmmmm Um No

: It's the combination of those qualities that turn Spartans into something
: truly awesome. Pit a Spartan team up against the Avengers, and the only
: one I'm not sure they can take is Thor.

Unless they keep Thor away from his hammer.
The hammer is a mix of tech and magic. Cortana would hack the tech side in seconds. Thor is no god, but an Asguardian often mistaken for a god due to his Hammer's abilities. Keeping the hammer from Thor would be the tricky part. Unless of course it sees John worthy of yelding it as well. In which case, Thor is utterly screwed.