The Scenario
Greater Sci-Fi combatant
So, how about that "protection from Twilight" thing the Master Sword showed? With some help from the Triforce of Courage, Link does have proven supernatural resistances that do not affect only evil effects. Until the Soul Eater shows some way to pierce that resistance, I'm leaning towards the Master Sword no selling its ability.
As for fighting ability, skill is indeed difficult to quantify. Which is why I won't try and instead give Link's abilities:
Ocarina of Time
http://www.youtube.com/watch?v=48AEDFgH4jY#t=3m42s
Link's strength with Golden Gauntlets is through the roof. Enough to make up for a skill difference? Maybe, maybe not, but that would be rather difficult to block.
Wind Waker
http://www.youtube.com/watch?v=lkS1GFQhldc#t=2m48s
Similar item, but a little less strength. Still wouldn't want him to hit you, though.
Twilight Princess
http://www.youtube.com/watch?v=AE6x19jE6Vk#t=1m6s
http://www.youtube.com/watch?v=rAJACleGuOs#t=4m37s
Twilight Princess Link is unique for being freakishly strong without an item, which is pretty nice. Tossing armored guys made of rock and large icebergs around is some good strength.
Skyward Sword
This one is more powerscaling, I freely admit.
http://www.youtube.com/watch?v=hJBMUyekvhk#t=28s
Ghirahim is capable of blowing through large stone walls in his weakest form. By the end of the game, Link can overpower Ghirahim's strongest form, often knocking him off balance when they clash.
http://www.youtube.com/watch?v=qHtO9q7s66o#t=4m9s