Samus probably smells bad. I mean, if you consider what she goes through, would she be any better than what the consensus graded Link? At her cleanest level of her Varia Suit, she might smell not to different from Mega Man with metal and electronics scent. But during and after battle, she's going to reek off singed wire & metal, sparks, camphor & smoke from explosives, plasma, and all the goo and viscera despoiled from all the alien creatures she blasts up. That suit is regularly exposed to lava, moisture, acid, ice, fungus, and water, with that last one not doing much to clean her stench. The area where the water is located would also seep its stenches and minerals into it. So an area like Marida could be akin to a pungent pond maybe with some sulfuric, decaying smell. Oh, and what if Samus is exposed to or infected with Phazon? I'd imagine it having a potent chemical, crystalline smell that would repulse upon contact with the nostrils just because of the threatening feelings it evokes.
Zero Suit Samus would be a much different story, however. Let's save her for another time.