So I just posted this all to some of the other Samus players but MK is my secondary so I suppose I can give some incite on the Samus vs MK matchup here.
Pros for Samus:
-MK can't do ANYTHING about projectiles. He isn't like Falcon or Marth that can just Nair/Fair through missiles and beat the pressure on approach. MK is forced to avoid everything you throw at him.
-MK's recovery is very punishable and gimpable. While MK has a very long recovery it isn't necessarily good. All of his recovery moves are very easy to knock him out of, drill (Side-B) can be CC'd and almost impossible to sweetspot so D-Tilt beats it pretty easily. Tornado (Neutra-B) just sucks in PM no real other way of putting it you can get good height off of it and really is the only solid vertical recovery he has (I know sad right), cape (Down-B) is the worst teleports in the game, he gets no intangibility off of it, tons of landing lag and kind of hard to sweetspot with especially from below, shuttle loop (Up-B) if you get knocked out of glide by anything you loose it, it is one of the worst glides in the game as well (probably the worst) they just screwed this move up HARD, I just want them to give him his S4 up-B personally. So basically all Samus needs to do is shoot some missiles off stage (homing are preferred imo) lay a bomb on the edge when they get close and wait for the terrible recovery option. Not the mention MK has no reliable meteor cancel option he's actually kind of like Bowser/DK so if you smack him with a Dair he's usually toast.
-MK is a REALLY bad weight/fall speed for kill options. If their DI is even slightly off D-Throw into any kill option will almost always connect at kill percents (also haven't really impremented it a ton in my playstyle yet but I'm confident Jab>kill option is pretty guaranteed on MK). MK is in such a weird spot on the weight/fall speed chart kind of the opposite of Samus really light but falls fast. Turns out though this is pretty bad for him since he doesn't fall as fast as spacies but is a lot lighter then them so he just kind of gets thrashed by any solid kill move.
-MK is weak to crouch cancelling. This is not a surprise, he got a new tool with Dair recently but basically everything else can be CC punished. His most common approach tools (fair, nair, ftilt, dtilt, upair) can all be CC'd (except initial hits of Nair but for that they literally have to be directly on top of you and why aren't you shielding) He is also pretty weak to OoS options since a lot of his aerials have a decent amount of endlag and little shield stun so Screwattack is a go to almost all the time. Up-Smash (especially Ice) can work as well but since they're a little slower you need to make sure your on point with your timing.
So yeah wrap up of all that: Projectiles screw him, punish his recovery, get your kill options thanks to his weight/fall speed, CC screws him even harder.
Pro's for MK:
-MK beats anything Samus has in the air. That's just the style of his character, his aerials can just ignore anything you got going on since Samus really has no disjoints (Fair a little I guess?)
-MK can kill very early. If your DI isn't on point and the MK is good at sweetspotting his Up-Airs (which is not hard to do) you can easily find yourself being juggled into an Up-B and depending on the stage you may die absurdly early. Yoshi's and Wario Land (especially Wario) don't be surprised to die at like 40% if you got bad DI. PS2 a Samus staple also has a super low ceiling so again watch out there.
-MK has amazing edguearding especially vs Samus' tether. Don't need to really touch to much on this since I'm sure you all know. Nair is amazing vs tethers, Bair can go out and challenge your bomb jumps without fear, and he has plenty of options to punish a forced getup off ledge like Nair Dair or even normal getup Dsmash or Fsmash if they're fast with it.
-MK has an amazing grab and dash dance. While MK's DD game is hurt by the projectiles he can still use it exceptionally well when he gets the chance. His grab is also amazing, it has surprising range especially boost and pivot grab (pivot grab is enormous PMDT please don't touch I like it) and while he cant get a lot out of his grabs anymore they still can rack up good damage fast if you got bad DI and get chain grabbed for a bit. His bthrow can kind of be used for a mixup but its not as strong anymore since the iasa frames were nerfed so he cant act out of it fast anymore. Upthrow is really stong and at mid percents on samus can lead into a kill option with bad DI (just go up and away or strait away always) no DI or up can lead into an shuttleloop or cape, back di can lead into a bair. At high percents though you don't need to worry about his throws that much anymore thanks to Samus being awesome.
-MK has a pretty good CC aswell. His Dsmash comes out on frame 4 and can kill and his dtilt is just like Roys which can pop you up for juggles so be careful with your pressure you don't wana be killed because your not respecting his CC like he should be respecting yours.
-MK really has no bad stage. This is just in my opinion but I never feel disadvantaged on any stage. MK can pretty much fight anywhere and I guess that's why I like him as my secondary. I personally don't like stages like Yoshi's Story, Wario Land and GHZ with Samus but for MK those stages are my favorites (especially GHZ
anyway so wrapup from this part: Beats Samus in the air, solid edgeguarding, amazing DD and grabs, good CC, and no bad stages.
I can see why people think MK looses to Samus and vice-versa but to me its almost even but with a slight advantage to Samus because of all her solid anti-MK tools.