Well, that's just a necessity. The game wouldn't work otherwise.
The game would however work perfectly fine if Ganondorf wasn't somehow weaker in every respect compared to Snake, although the former is a warlock with the power to singlehandedly overthrow a whole country and who can't actually be hurt without the Sword of Evil's Bane, while the latter actually has to avoid any conflict because he can easily be overwhelmed by a bunch of random mooks, or how Metaknight's cute little flip in the air, or, well, basically ANYTHING is stronger than Samus' nair, or, Game&Watch... just Game&Watch.
The game would however work perfectly fine if Ganondorf wasn't somehow weaker in every respect compared to Snake, although the former is a warlock with the power to singlehandedly overthrow a whole country and who can't actually be hurt without the Sword of Evil's Bane, while the latter actually has to avoid any conflict because he can easily be overwhelmed by a bunch of random mooks, or how Metaknight's cute little flip in the air, or, well, basically ANYTHING is stronger than Samus' nair, or, Game&Watch... just Game&Watch.