LMAO!!!!!!
I can't believe I missed all of this.
Anyway.
Reasoning:
Link has PLENTY of tools that would be advantageous to this fight. Though I'm not familiar with every name for every item, he's got things that make him invincible, invisible, powerful, bigger, faster, stronger, and tougher. Light Arrows are a VERY good offense. Cane of Byrna is an extremely good defense. With these, and other various items, Link has plenty of options to make this a fair fight, if not in his favor.
HOWEVER!
The reason Link losses this fight is not because he's not strong enough or fast enough or motivated enough or TriForced enough. It's because he would ultimately lose in a battle of tactics. Links fatal flaws are those of stamina and range. The only problem Samus might have are dealing with light arrows. Assuming these bad boys are lethal to our space girl, shed have to dodge these while shooting back, or simply running away until link depletes his supply. ALSM stated that link can have up to 100 arrows at once, so a smart Samus would be dodging and firing back, be it plasma beams, hyper beams, wave beams, or her phazon induced gattling lookin charge shot. Links second fatal flaw is that he cannot have more than one item out at a time, save for shield and sword. And if any beams did not work against the shield, missiles are the next best bet. It's a well known fact that in Zelda games, you still get hurt for trying to shield explosions. And since the mirror shield only reflects beams of light and whatever, the explosions of missiles would hurt link because of blast radius and/or the encasing of ice, since the missiles do get upgraded to ice missiles. And links third fatal flaw is that, with all his magic and many varies and potions at his disposal, they are greatly limited in amount compared to samus' arsenal. Link gets hurt, fairy. Link runs out magic, potion. Rinse and repeat. But how many times does this grant him? Eight refills depending on what's in links bottles. This means he'd have to distribute between how he'd be supplied for battle. And even then, samus' superior range and speed of attacks would force him to use his supplies quickly, or suffer being defeated right off the bat. Samus' ship is also usable via remote control from her suit, giving yet another powerful stance that is movable from a far range, thus making the fight two one from various locations, and even being able to excite a pincer like movement with the use of the ship to corner link and force even more usage of supplies or making a rash decision to avoid harm.
This battle is decided in who is more prepared for a long, drawn out, battleship type war. Long range, mid range, and close range, samus excels in having one or two weapons that put link in bad situation.
Both games are fun, great. Both heroes are awesome. Both of them suck in brawl. But in a smarter world, which is where our heroes would meet, Samus would win.