Ugh this is a toughy. Mario is the best "classic" protagonist, but Samus is the best in the sense she handles business. She owns everything haha killing enemies stronger, larger, and armies more menacing than anything in the Halo franchise even.
But when it boils down to it,
My vote has to go for Link. The best Legend of Zelda games are all about a boy starting a journey and ending it evolving into a man, or in some way maturing in the process. He never asks for nothing, but the weight of the world always rests on his shoulders.
Link is my choice.