I can't say that Mario or Doc are much of a threat. Samus has a larger frame than them so that can cancle any close in approaches that they may attempt. Samus tends to have a little trouble getting those easy kills from gimped recoveries on them because of her lack of good horizontal finishers but if you play "attack" with good spammed Nairs and tilts, then they can be confined and done away with.
I find Falcons and Peachs are easy to contain, and Marth may have the tool-of-renduring-missiles-useless but that isn't enough for Samus to be overwhelmed by.
Falcos and Foxs can be torn apart with well placed tilts and aerials. Her down and up B resist any possible dashing approach, comboing and pillaring attemps. They're tamable.
I think Sheik is the most common threat. For the obvious reasons if anything.
I'll also go out of the comfort zone and say Kirby. A well played Kirby gives Samus nightmares!!!!
Missiles won't do anything if the Kirby is aware, his Dair and Cides will finish Samus EVERYTIME she is knocked off stage. Kirbys tilts are destructive and a head-on approach is actually effective.
Samus can edgegurad well with missiles and her Fsmash is one of the only effecient ways of finishing Kirby. Though Kirby can simply crouch under it if the smash isn't directed to the ground. Samus can't quite match Kirby in the air unless the battle is simple and subdued with Nairs, which is difficult when Kirby can react with a larger priority Fair (which can eliminate projectiles as well as Marth) or Bair. Samus sheild-Upb doesn't have much use here but her dsmash and ftilt can make up for that enough.
Kirby and Sheik, other than that, Samus can take care of herself
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I also find YLink can spam projectiles well, and that can hurt an unagressive Samus.