Okay, here is my new-gument:
Samus can pretty much one-shot with her normal attacks (Ice, wave, spazer, plasma and chargerd beam are OHK) and she has far better range, plus some degree of time and space manipulation and a lot of other broken abilities.
Guardian on the other hand is not that, helpless, he can constantly weaken her by life draining her, make her bleed out, suck her soul until she become a pale creature, paralyze her with melee attacks etc, he will able to heal normal wound (If there any normal wound), become more stronger by absorbing her life-force and soul, and become inmune to her attacks.
This is not a stomp, is more a "Who throw the best cards first", Guardian certanly has the ways to kill her, but I think that Samus is going to win in the mid way, seeing that she has a lot of her best cards in her normal attacks, and Guardian seems to not be able to use multiple of his abilities a the same time.
I will go with Samus, mid difficultie.