Increased weight
Ganondorf's weight is 113. Samus' is 108. Suppose that since Samus in Metroid: Other M is shorter than previously thought, a woman who stands at approximately 1.75 m. she should have a mass of 66 kg. If the armor itself is 90 kg. based on the now outdated Metroid II: Return of Samus manual, then Samus' mass is 156 kg. with the armor on. Ganondorf, who stands at 2.29 m. (Hyrule Historia) has a mass of approximately 130 kg. With an additional 10% based on Hamwi's method, he should have a mass of 143 kg. With a percent difference, Samus' weight should be 122, while Ganondorf's remains at 113. This would actually put Samus' weight exactly at Donkey Kong's. Of course, since in fiction, Donkey Kong has a mass of 363 kg., I don't see Samus being equal to him. So even with a weight of 114, I'd be fine with that. Of course, weight and fall speed aren't the same, so Samus shouldn't end up being combo food like Bowser or Donkey Kong.
Air speed and acceleration
I wonder what it'd look like if Samus had better air speed on par with Zero Suit Samus. Maybe that would seem too fast. Perhaps lower than Zero Suit Samus, but maybe about as good as Sheik's. I wonder what that would look like. If it seemed too fast for Samus to the point her controls weren't optimal, then maybe decrease it somewhat to a point where it's tolerable. Of course, with improved air speed, that probably would be best to include its acceleration.
Run speed
I don't think running is all its cracked up to be, and while I thought maybe putting Samus' running on par with Zero Suit Samus' was a good idea, maybe it's not. I find it sad that two super-heavy characters like Bowser and Donkey Kong outrun Samus. What if Samus' run speed was at least as good as Mario's? Since the suit actually improves Samus' athleticism, and since she does acquire the speed booster, it'd be nice for a faster Samus.
All aerials auto-cancel
This might seem absurd, but in Brawl, this was a good thing for Samus. She was able to perform short hop homing missile cancel, allowing her to fire an additional missile to build a wall. In Sm4sh, this is nowhere to be found.
Crawling
I'd like to see Samus use her morph ball. Not only could she dodge certain projectiles, characters who can crawl are able to space themselves when the opponent is on the ledge, allowing them to find an opening for the opponent's error. Not to mention, the morph ball is one of the most iconic abilities in gaming history.
A roll with fewer frames
If the morph ball does one thing, it actually speeds up Samus' movement compared to crawling. We can observe this in Metroid: Zero Mission, where when Samus crawls, space pirates who also crawl after her can keep up. Yet, with the morph ball, she leaves them in the dust. So, fewer frames for a roll would be nice. Rolling wouldn't be so bad for Samus players.
An additional jump
Pit, who is canonically incapable of flight, can perform multiple jumps, whereas Samus is stuck to a double jump to screw attack. The space jump allows Samus to jump infinitely, but all I would like is a third jump.
Faster grab and less lag when retracting the beam
This and
that speak for themselves.
Increased hit stun
I'd be nice if Samus' jabs had hit stun. It makes no sense as to why Zero Suit Samus has hit stun with her jabs, where her armored counter-part doesn't. Come on, Nintendo. Armor means better.
"Harder, better, faster, stronger" super missiles
It's sad to see homing missiles easily destroyed by a jab, but even if it wants to function that way, I think super missiles deserve to be, well, super. Make it so that super missiles aren't destroyed by Link's arrows or gale boomerang. Make it so that stronger attacks are required to destroy super missiles like a smash attack, or shadow ball, or aura sphere. It's great that charge shots destroy super missiles and keep going, but super missiles should be able to take more punishment. More speed like in Melee would be great, too. Its knockback would also be fantastic like in Melee.
More kill moves
In Melee, down smash could KO. In Brawl, down tilt could KO. These should make a comeback. Samus needs more kill moves. She can KO with a full charge shot, n-air (I love the new n-air), b-air, u-smash, and possibly screw attack, but even the screw attack doesn't mean much. And don't bother bringing up the shinespark method because that's not as easy to perform as it sounds. It's also limited on percentage of the opponent and the stage. B-air is difficult to KO a grounded opponent because the landing lag leaves Samus open. Zero Suit Samus, on the other hand, is pretty safe. I'd love to see something like that.
Fix d-air
D-air serves one purpose, and that's to spike. I don't like these sour spots for it. Let it be old-school and do what it's meant to do.
Fix f-smash
This attack still whiffs, believe it or not. That needs to be fixed.
Fix u-smash
It annoys me that Link's u-smash will remain connected to the opponent if the opponent happens to get hit by the first part of u-smash. Why is it that Samus' u-smash can't do the same? It's not an issue of DI. It's just an issue with the attack itself. I think it should be like Link's u-smash.
Kill throws
It seems like everyone has a kill throw, especially when these characters never demonstrated such strength to throw people like rag dolls. Marth's up throw shouldn't happen, for example. Olimar's forward throw? Since when can this little man kill by throwing?
Samus at least has demonstrated such strength. That there could be applied for Samus' back throw. Her up throw should also kill, since she throws Vorash up into the air. Let's think about this. Vorash is about the size of a whale shark, which has the average mass of 21 metric tons. Remove the density and we end up with a volume. Now, since Vorash is swimming in magma, which is far more viscous than water, that would require greater density on Vorash's part. Otherwise, he'd just be atop the magma. This means that with a density of 2.45 g/cm^3 (andesitic magma density), Vorash's mass goes at least close to 50 metric tons, and that's ignoring the layer of magma added to him, as well as those fins of his. So 50 metric tons is a reasonable approximation. Samus needs kill throws. After all, if she's not going to have a good grab, she may as well be rewarded for taking a risk. So, either kill throws or better grab. I'm thinking the former is better.
Bombs
I'd be nice if they behaved like proximity bombs like in Melee.