Remember she also has no kill power so make sure you don't lose those stocks until you're pushing 180%.
For her projectiles, make sure you powershield everything she throws out. This is one match-up where being mobile and approaching is beneficial. Know her habits in which she shoots her projectiles. Usually a kill set-up she'll fire two or three missiles of varying type (super missiles and heat seekers) and fire a fully charged charge beam. Your grenades beat a lot of her projectiles and I believe you can jab heat seekers (missiles have HORRIBLE priority by the way). Also, watch the spacing of her zair because a fully extended zair will deal 7% (3% more than any other hit of it) and will deal high knockback.
If you're off stage recover high as to not get spiked. None of her moves break cypher other than spike I believe. Her other aerials are alright, bair is considered one of her kill moves, and fair is used for returning on stage from the ledge. Remember she has a sex kick as well so watch out for that. An approach Samus's use is u-air (always auto cancels and gains priority the longer it stay out) to f-smash or d-smash.
The only things Snake really needs to worry about in this match-up is the edge game (NEVER challenge a planking Samus she has an above-average edge game) and the zair. Zair has amazing range and auto cancels so Samus can do many combos out of it.
Remember though, she has no answer for that f-tilt of yours (as long as you're not terribly predictable) and u-tilt has ******** range on her. If I remember correctly, when you d-throw Samus you can crouch to avoid her get-up attack and stop her back roll so that further limits her options.
Edit: Sorry for the wall of text.
