Samus I think somewhat accurately captures how she was in her appearances in the early Metroid series like Super Metroid. Movement there was pretty floaty, and she didn’t necessarily zoom around like she does in Metroid Samus Returns and Metroid Dread. However, with the direction of the character moving toward a more action focus, even as far back as her appearance in Metroid: Other M (or even Metroid Prime), her movement has become a lot more fluid, and it’s hard to say that her current gamefeel stacks up.
In terms of how her arsenal is included, I think it works well. Most of her different armaments are more akin to ammunition types than different abilities, and the ones that are different are all present and accounted for aside from her new Aeon abilities, and the psionics in Metroid Prime 4: Beyond…not that I really want her free controlling her Charge Shot like she’s Pit or something.
I think what a lot of people find off about her moveset is how it distributes power between her melee strikes and projectiles instead of focusing on the projectiles specifically. Looking at Mega Man, he’s able to fire his primary weapon with ease, and his whole kit is built around that new control scheme, while Samus’s primary weapon is just a neutral special, and while its power incentivizes it’s use, it’s not quite as versatile as the Mega Buster. That being said, it’s also a very different attack from the Mega Buster in cannon due to its omnidirectionality. Giving Samus the ability to fire her beam in 8 directions while preserving her fluid movement would be difficult with just one button, and doing so with multiple buttons would make her entire moveset just 1 move, which would not be popular. And then the missiles would be just the same move, but with more damage.
Many moveset reworks for Samus give her the ability to swap weapons as well, allowing her more utility with the use of more of her munitions, but they either require the use of a taunt button, which I don’t think should ever be used for a critical moveset feature, or a menu, which really doesn’t belong on a character that’s supposed to be fluid to control.
Samus is definitely one of the cases where a 1-1 recreation of their abilities does more harm than good, especially since her fighting style is “run away until the opponent overextends, then pump them full of lead and energy blasts”, which would make her a character that is overwhelming to fight, and either have no weaknesses, or be extremely exploitable with a very narrow window of balance, and a high amount of frustration even in that balanced state.
If we’re going to modernize this kit, I think the way to do it would be to raise her fall speed so that her vertical movements are fluid, but keep her gravity low so she can still linger in the air should she need to, and so she doesn’t drop like a rock off stage, as her recovery would not be able to handle that. After that, incorporate her main beam into more of her normal attacks, potentially replacing all of her weird point-blank explosion moves. This could end up giving her keep-away tools she doesn’t necessarily need, but would improve her gamefeel as a run and gun character, so it would be worth adjusting other areas of her kit for this feature, and I’m fairly confident in saying this because these attacks on Mii Gunner have caused remarks of them feeling like Samus should (even if they’re uncommon because most people don’t talk about Mii Gunner).
After having used it in her two newest 2D games, the Melee Counter feels like it should be a staple of Samus’s moveset in Smash, allowing Samus to check approaches. I’m not sure you should make it a special move, but having it as a couple of her normals should be just fine. As for the other special moves, I’m cool with them as is, but if they need to be changed to accommodate a new set of normals, I’d be fine with that too.
Also, allow her to crawl with the Morph Ball, and maybe even jump around in Morph Ball mode if the player holds down or something. It would be totally useless, but it would also be a cute touch, and it feels like something we should be able to do in the first place. I’d also like to see some better characterization from an appeal standpoint on Samus. I know this isn’t a character that emotes much, but a lot of her taunts and victory animations are a kinda nothing. As a minor nitpick, I’d like to see her dash attack more accurately reference the shinespark by having her crouch at the start of the move, and cooler effects work added to the move itself.
Lastly, I have seen complaints about her doing physical attacks at all (some about up air specifically, others about her neutral air, and some about arm cannon smacks), and while I think this was mainly a thing before Melee Counter I would agree that some of her physical attacks are a bit odd. I don’t hate them enough to want them replaced, but her neutral air is kinda weird if you think about it for more than two seconds.