As a puff player who uses Samus as a secondary, I'm pretty good at dealing with the MU. One of the biggest issues is Samus -can- out-air you if they're good. You really don't want to be above samus, ever. Samus also has a horrible roll that is very easy to punish. If they're rolling a lot(like you mentioned), take advantage of it. As said, if they're rolling away from you, extend your dashes, or prepare for them to roll before throwing out your aerials, throwing another jump in before you attack. The projectiles themselves are fairly easy to dodge as puff. Doesn't make them any less annoying though.
when facing samus:
Dashing(Shoulder Tackle and Grapple are both threats): I usually just nair, but make sure I clear the grapple.
U-air: Hit box is basically samus's entire body. Has a slight lag window after ending before samus can do anything else, but it's small so if you aren't already right by her, find a better opening.
Fair: Try and air dodge through her and hit her with an aerial if you see this coming. She's wide open while performing it, as long as you don't approach from the front.
Bair: Like puffs, but more reach. it can kill from roughly the same %s and has the same flaws.
Dair: your typical meteor, same drawbacks.
Nair: Hits in the front rather quickly before swinging to the back.You usually won't have to worry about this.
U-tilt: It's fast and at low %s can be chained together and closed with a charge blast. Being directly in front of samus when she is able to act is dangerous. There really isn't enough end lag to punish this with puff unless it just barely misses your approach, or you shield it.
F-tilt: Good reach, and fast. Same as u-tilt, if you aren't already in a good position to counter it, you probably won't.
F-smash: the endlag on this is fairly noticeable, but it's still fast and a threat.
Down-tilt: Fast and kills, but is about as punishable as an f-smash.
Up-smash can be a nuisance if you like to approach from the air, but it's avoidable and punishable.
Be very wary of super missiles while samus has a full charge beam stored, as shielding a super missile + a charge beam will shield break. Usually better to jump over missiles or just eat it, as the knockback from the missile will clear you from any followup.
Screw Attack can kill, and puff will usually die to it around 120% or so, maybe 130%. This leads back to the "You do NOT want to be above samus"
Bombs are a nuisance, but easily avoidable. If samus is using them on the ground to hinder your dash attacks, SH over them and use an aerial.
The general thing to remember- Samus's moves come out fast, but most have end lag, and she is very vulnerable while rolling. Bait and hit. You have to try and read which method they're going to use to protect themselves(tilt, aerial, roll, whatever) and punish it. If you get too aggressive, you're going to play right into samus's strength.
(fyi, I'm horrible at advice, better at showing. Anyone with better advice, feel free to correct me.)
