I agree Samus moveset feels kinda outdated/uninspired, would be cool to see her play more like in Metroid games.
Personally i would change Neutral B to her charge beam which would function like it does in for example Super Metroid.
Could be rapid fired similiar to Falco's lasers if B button is tapped and if you hold B you could charge it to different levels before releasing while being able to move as well as aim in different directions at the same time.
(Maybe also stored like in it's current form if charged fully but would probably be unbalanced with the aiming)
Down B could be changed to go in and out of Morphball mode where you could lay bombs with maybe neutral or down B and use Boost Ball using Side B. Could keep the high aerial acceleration like in it's current form. Alternatively you could make her crawl the morphball mode and leave Down B for something else.
idk haven't played the Prime games but it feels like there's lot's of untapped moveset potential for Samus as she has used so many gadgets throughout the years since Smash 64 was made