As swordskill goes, I'd say they are pretty even. I'd say that Link might be at an advantage (since in Twi he is trained by an elite swordsman) but Isaac also crossed blade with very skilled swordmen (Saturos, the Colosso fighters who are basically the best non-adept fighters of the continent). Isaac's abilities are also strongly affected by his djinn setup, I'd assume that using them to get to the Ronin or Master class he gets a much better mastery of his blade (on top of higher physical abilities in general) than when in his normal Knight/Lord class. So in that case it really depends on the setup, for the sake of fairness I'd say none of them had time to prepare, so Isaac is just going mono-element. In that case they are more or less even as swordsmen.
As far as physical strength goes, I'd give an advantage to link for lifting strength (because the massive metal ball he lifts and all) but other than that, given the boost from the djinns, I think they are again more or less even. Isaac can lift as many of those balls as he wants with psynergy tho', but it doesn't have much use in battle aside from moving them around (same for Link, lifting them isn't very useful in a fight)
What really affects how the fight will go is the other abilities and arsenal, and I have to give Isaac a huge point here. Even locked in Earth manipulation it's a big advantage already. Creating pits, stone pillars, stone pikes to launch like ballista shots or just make the ground implode is impressive and all, but it is especially effective to control the battlefield and create a favorable terrain. Then he has his healing abilities, and they are very high. He'd just need 2 or 3 seconds to heal almost all of his wounds, that would push Link to be very aggressive to not give him the occasion, but then again, Isaac can create so many obstacles. Link does have a bunch of items tho'. He could try to place bombs to surprise Isaac, leaving them behind a rock or dead angle among the rubble and all. Or explode obstacles to reach him. The bow also gives a good ranged option to create an opening if he aims well. The clawhooks also give some manoeuvrability which could get handy if the terrain gets full of rocks and pillars (or maybe even a lot of floating boulder that could be used to hinder bow shots etc, but then link could grapple to them to get to a high position). I am not sure what else in TwiLink arsenal could be useful though.
Then there is the djinns, if Isaac is allowed to use them it would probably be the deadliest options available, to the cost of weakening him for a time (which would create an opportunity for link, and a nice tension in the fight) but open up for a summon which could end the fight instantly. Going for the Venus(earth djinns) Isaac could use Flint (wouldn't destroy the Hylian shield but would definitely break Link's guard), Granite to halve the damage of an attack he couldn't avoid, Humus to flatten Link of the ground for a few seconds etc. Most of them would be used as defensive buffes to make him even tankier. I don't think summons are allowed, but if they are, after 4 djinn used, Link would have to end Isaac very quickly or he'll take a country/continent wide explosion to the face.
So yeah, my vote goes to Isaac's win on that one. Both of them are pretty smart (solves lot of puzzles and all) so they'd probably attempt a wide array of tactics during the fight to try to corner the other.
