Honestly I'm pulling for Big Boss in this one. I was all about Link before, but this is the type of battle where a strategist would have my vote.
Wolverine doesn't have a one track mind, he has a one rail mind. When it comes to planning for a fight, he just figures that he'll roar with fury and slash apart whatever's in front of him.
Link is borderline brain damaged. You'd think that after dealing with all he's had to deal with, things wouldn't shock him. But no, things shock him a lot. He does his "Oh my god!" face when confronted with a boss battle. He typically prevails, but mainly because those bosses flaunt their weaknesses or are terribly vulnerable to one particular item.
Big Boss finds himself taking on two opponents who are insanely powerful in their own right, and who both suffer from
power induced stupidity. He has the ability to cloak until he's practically one with the scenery, and he can hold his breath for an obscenely long amount of time.
Wolverine has survived a hell of a lot, and his healing power would be unknown to Link. Link is one resilient mother fucker, and his fairy in a bottle that can resurrect him would be unknown to Wolverine.
Here's how I see this fight playing out:
Big Boss knows that he'll be easy pickings if he engages either opponent as he'll be vulnerable to a flank, so he lays low and observes. He already knows Link well enough, having suffered a draw against him. Big Boss is wise enough at this point to know that any future opponents require a double tap, even if they took a head shot.
Link and Wolverine encounter each other, neither man at all concerned with the absence of their other opponent. Wolverine's claws deflect off of the Hylian shield, leaving Wolverine prone to a thrust through the rib cage by the Master Sword. Wolverine goes down with the Master Sword embedded in his chest. Link approaches to pull the sword, and his head erupts from Big Boss' sniper bullet. Link resurrects, Wolverine takes cover in a weakened state and removes the Master Sword from his chest. Automatic fire suddenly distracts both men, keeping Wolverine and Link pinned down. The bullets stop coming after only a few seconds. Link takes cover with the Hylian shield and charges toward where the gunfire was coming from, only to step on a claymore mine and become pieces of his former self. Wolverine charges with claws out to the gun nest, while the rank flesh of pieces of Link that scatter the area cause his sense of smell to become distracted. He finds a mounted assault rifle which was rigged to fire until the expanded clip had expired. While in a brief state of confusion, a knife is raked across his eyes by Big Boss from behind. Wolverine takes a knee and swipes his claws wildly around him, needing to take a few moments for his eyes to heal. A flash bang goes off next to Wolverine, causing him to hear only a low tone. Wolverine panics, and freezes in place.
Big Boss shoots Wolverine in the eye at point blank range, and jams another flash-bang into his eye socket before taking cover.
Vote Big Boss.