While Kratos seems to have more skill with his primary weapon, Link has a greater variety of skills/weapons (i.e. bombs and the boomerang). Link also has a greater ability to manipulate the enviroment. In short, Kratos probably (but by no means certanly)wins in a non-manipulatable enviroment (though Epona could shift this in Link's favor). In a manipulatable enviroment, Link would probably win.
Link has a piece of the triforce, which makes him powerful