Stealth Moose
Umbrella Elite
They're very good. Unless Snake gets tons of intel and prep and EMP's, I don't see this going in his favor in anything but maybe the sneaking.
Jensen's augs are passive and released through software upgrades or over time. It's stated by the LIMB clinic doctor that all the augs he has will unlock eventually, meaning in theory AJ can use any and all augs the game allows.
This means he can effectively cloak, punch through walls, elbow blade things to death, defy gravity, hack remotely using his augs controlling bots and cameras, have inhuman aim due to steadiness/aim augs, improved jumping, running, stealth running/jumping, etc. etc.
In H2H, Snake has more experience, but Jensen has more physical strength in his arms and legs which are augmented. Considering he can punch through walls and snap necks with little effort, this goes to him.
In firearms, again experience goes to Snake, but Jensen's augs help him here. He has uncanny accuracy and regenerates with his Sentinel implant. Unless Snake gets the drop on AJ, the aug wins.
In sneaking? Experience to Snake, but unless Jensen is robbed of all of his sneaking augs (which allow him to run, jump, and walk without making a sound) and his cloak (which makes him invisible), I don't see this being conclusively in snake's favor. It boils down to variables like the map, and what's the obstacles.