Fourth hit of dair -> stick is great if they get popped up, otherwise you can jab reset for the tranq/stick. Any other hit can work but isn't guaranteed and will probably get you hit (but it's usually worth it).
[ftilt 1 ->] jab reset -> tranq [or stick or grab] is also really good, which usually lets you stick and grab.
Uthrow -> SH Stick works at low percents (it'll trade at the very least, but you could wavebounce it). Dair tends to link well from Uthrow too, which brings up the first option.
Cypher to Stick works if they don't DI behind.
Crawl tilt -> grab works better than stick because of the possible followups listed above and is really good since it mitigates missiles and most charge shots.
Consider c4 to punish grapple recoveries. I haven't tried it myself much, but I do believe they're vulnerable until they actually grab ledge, so detonating a dropped c4 could pop them up for a fair or dair spike/meteor. Grenades can also work.
Placing mines on platforms could be good for you, since Samus doesn't depend as much on movement as Snake does.
It's really just fundamental Snake things: what I noticed about Fire's match vs. Xion is that Fire didn't pick up on Xion's ledge habits: the mine on edge is beat out by roll on stage, which Xion did a lot but Fire never punished with something like ftilt, utilt, grab, stick, etc. or invincible getup, which can be tranq'd. Tighter DI reads could've given an extended combo right off the bat for game 1 as well with the initial uthrow to dair, and better punishes from those reads as well, like that tranq read on the roll at 4:38 which was punished with fair which led to an unsuccessful edgeguard which lets Samus reestablish the neutral game. It might be cheeky, but ftilt 1 -> jab reset -> retranq would work there to allow an easier stick setup into grab, as well as a stick outright. Fire also gets a lot of 4th hit dairs that Xion CCs which could've been jab reset in the second stock.
Fire also sets up another edgeguard this stock with the back throw off stage, but places a mine between himself and Xion, which just gives Xion the option of grabbing ledge and using the invinsibility to get back (which he actually fails to do, yet doesn't get punished for, which lets him fix his mistake). A better option that I've found has been to lay the mine, but then wavedash to ledge so that Samus has less options to recover, but that could just be my Sheik play seeping into my Snake play. This way, you can bair a lot of Samus's options offstage, or force her into the mine on stage, or into an unfavorable position out of the forced tether jump from ledge. All the while, you can roll to avoid getting hit by your own mine. This situation arises again at 8:18, which leads to the same situation AGAIN at 8:30, and at 9:06 as well.
The down throw at 6:25 feels questionable as well: Samus is at a percent where the pummel damage isn't as important as setting up a good tech chase for a KO. With the C4 on stage already, Fire could've walked Samus to the right to set up for a C4 KO if Xion rolled left, which makes it more likely for the getup attack, which could be grabbed to reset the scenario in a better position; or a roll right, which sets up for a fair KO off the side (probably with the help of tranq). Regardless, the mine placement was ill-timed and he got punished for it (even though Xion failed to edgeguard).
The Powershielded missile -> Grab at 7:00 was so clean, but got ruined by the pummel (which never works below ~35% if you opponent mashes). The general rule is that you get one pummel per 35%, so be conscious of their behavior out of grabs so you'll know whether they mash or not. A quick throw in this situation might not have gotten the best of DI, which means a stick or dair followup would've been possible at the low percent.
The rest of the match is more minor things: It also looks like (based on 7:27) that tranq pierces through missiles and remains active afterward, as Xion fired a missile and got hit by the tranq, so that could be an option if you manage to get into range. at 7:52 Fire shields a downsmash, but wavedashes back to reset neutral. Wavedash forward is probably better due to the ending lag on downtilt, which Xion was clearly worried about based on his own wavedash back. Samus's neutral game is stronger than Snake's, so trying to get to neutral in this matchup isn't that great. The down tilt to fair at 7:56 is questionable as well: I don't believe it works on Samus at all, let alone at over 100%—grenade zoning or juggling with quick Cyphers and uairs would be preferable here. The cross-up dair at 8:00 could've squeezed in a stick or grab. That 8:35 grenade could've been hit confirmed into a pickup grenade into smash throw up instead of the upsmash, which would've KO'd. Frankly, FD was a really hard stage to play Samus on, so Fire did a solid job overall, but the edgeguarding is the glaring problem I saw.
Game 3 to WarioWare is much better stage-wise. That initial Cypher OoS should've gotten a C4 stick instead of the UpAir: it's an easy habit to throw the aerials. Sticks are easiest at the early percents. Xion could've been KO'd after the mine hit at 11:53 had Fire stuck Xion there. The tranq hit at 11:55 was tough as well, since there wasn't enough time to fair, which means there wasn't enough time to stick, so it feels like an empty tranq. I think if Fire had run up to stick, Xion would've rolled, so maybe tomahawk C4 would be good? It looks like Fire tried to C4 after the fair, but fair is just horrible on shield. Nair might be better for that specific situation. Fire's edgeguarding style for this stage is a lot better as well, since Samus is more comfortable jumping from ledge when there are platforms to go to, which are covered by the C4. I still feel as though being on ledge is more advantageous, though, as Xion only got KO'd because he forgot about the mine. The techchase fair at 13:10 was beautiful as well and is what I really wanted to see at 6:25. The platform camping in this third game is indicative of Snake's playstyle for this matchup, since he has so many projectiles that can hit below him, it's relatively safe, especially against Samus, who lacks a good upward aerial to hit Snake. The final stock has a lot of grabs which easily leads to a KO. The stage helped SO much here with the small blast zones and lack of camping ability for Samus, combined with Snake's ability to camp vertically and control the stage more powerfully. Fire considered the strengths and weaknesses of both characters and chose a stage that best complimented his own strengths, which made the game look so easy.