Why not? It's not like Super Smash Bros. is completely true to canon.
Anyway, I know Samus is a character who is currently present in Super Smash Bros. and has been since day one. Still, I think it would be interesting to make changes to character movesets as new games from a series developed. Link is an example of a character whose side special changed from an ordinary boomerang to a gale boomerang. This might have been done to avoid making Link and Toon Link too similar. Samus' d-tilt in the original Super Smash Bros. was a sweep kick, not a flamethrower. Donkey Kong's f-smash used to be a backhand, not two hands trying to crush his opponent. Captain Falcon's f-smash was a roundhouse kick, not an elbow to the face. I have a few ideas for Samus.
In Metroid: Samus Returns (MSR), Samus receives Aeion abilities. These include scan pulse, lightning armor, beam burst, and phase drift. I could see Samus having an Aeion gauge that she could activate. The thing about it is that unlike in MSR where Samus can use all four abilities at once, it'd probably be very limited here for both balance and because of the limited button inputs. Here's how I could see the four Aeion abilities working.
Scan Pulse: In MSR, scan pulse simply worked like a power bomb without the destruction. It would reveal unchecked areas on the map and expose hidden, breakable blocks on ceilings, walls, and floors. These objects would flash temporarily. This could transition in Super Smash Bros. by making the opponent's shield reduce in health, since this would be understood as Samus finding a weak point on the opponent. Alternatively, if that is an issue, the opponent could receive a bit more damage than usual.
Lightning Armor: In MSR, lightning armor protects Samus from many attacks. This doesn't include super-heated rooms or magma, probably to avoid the player from sequence breaking. After all, a flame is 1,000 °C. Magma can be as cool as 600 °C. So, either the magma is much hotter, or the developers didn't want the player to sequence break. I could see lightning armor working like Shulk's Monado Art Shield without the reduction of movement or attack damage.
Beam Burst: Beam burst would take Samus' ability from charging her charge shot, and instead make her neutral special behave much like Mii Gunner's forward smash. Just like in MSR, this Aeion ability would cause more damage and have a higher rate of fire.
Phase Drift: This Aeion ability would work like Bayonetta's witch time. That doesn't sound fun, but Samus isn't like Bayonetta, so she wouldn't be able to carry her opponent off to the ceiling. During this time, Samus could deal significant damage to her opponent. There's really not much else to be said about this ability.
That said, how would all of this work? Only one Aeion ability would be able to be used at a time. Once the Aeion gauge is activated, it remains activated until the gauge is gone. Furthermore, the gauge could only be activated once it's full. (In MSR, the gauge doesn't need to be full. It just needs Aeion energy to be usable. It can also be activated and deactivated whenever the player chooses.) The d-pad would be the method of activating the Aeion gauge. This is because the d-pad has been used in past and has been character-specific. Using the d-pad in Super Smash Bros. Brawl allowed Samus to become Zero Suit Samus, for example.