Why do I think this: Samus really didn't and doesn't have anything wrong with her. Seriously, she didn't. She mostly had number issues similar to Marth -- she still has some issues like her grab recoveries are atrocious even compared to ZSS's and some minor things like Down Smash isn't strong, so maybe it could have lower recovery to be a fast, but versatile Down Smash or just be strong and be a simple Down Smash or maybe her throws could do more damage. Off the top of my head Ftilt is one -- pre-patch it was a Brawl Ftilt with sour-spots -- and Nair being this average speed, but pretty weak aerial to an average speed, but pretty good aerial. Also, her dash attack kind of got buffed, but also kind of not. It was kind of reverted to its Brawl and Melee startup, but not its damage. She really does have an early hit on her dash attack since the clean hit could be considered the frame 10, 10% hit. Thinking about it, I don't really know why her dash attack had to be increased in startup from Brawl and Melee's 7 to launch Smash 4's 10. Now it's frame 8 and pretty fine. None of those dash attacks seem to be broken, but whatever. Animation-wise, pre-patch dash attack did make sense as a set and launch tackle similar to Ganondorf's Wizard's Foot, but yes, the setup having a hitbox as it's pretty much a shoulder bash does makes sense too. Anyway, I digress.
Samus is a character who can control space well; one part through her being naturally tall and with long-reaching limbs e.g. Ftilt, Nair, and Bair and the other part through her projectiles and disjoints -- this part is probably more of her Zair than anything. She pretty much has a reversal even if it's not as reliable as say, Mario or Ryu's, through Screw Attack, her recovery is pretty good mostly through her ability to shrink her hurtbox and weave about through Bomb and having access to a tether recovery to mix things up, and her edgeguard and ledge-game might be potent. Not sure since she has, like other characters, lingering aerials to edgeguard people, a low-hitting move to 2-3 frame people with Dtilt?, a strong ledge trump Bair shared with ZSS, and then there's the whole Bomb shenanigans. She also has a solid, stable and perhaps s flexible game plan unlike say, PAC-MAN where if you wreck his setups, he can't really do much or if, as many people say, zone Bayonetta out, she can't really do anything. Her major problems other than the whole "Samus sucks" thing spread by that video and her reputation as being "the worst character" deterring players from playing her at a high-level would probably be that yes, she's not fast. At worst, she's kind of like Mega Man. Not fast, but not slow. Samus's anti-air isn't that great either since Screw Attack is mostly vertical, Utilt's slow, and Up Smash has issues with connecting leaving her with mostly jab, angled Ftilt, and angled Side Smash for anti-airing -- air to air, she has Zair, but Nair, Fair, and Bair also work. There's also the whole roll issue. If only she had her Metroid: Prime dashes...
I don't know Samus, so I'll leave it at that. What I would like to know is the idea of her MU spread. I don't remember her being said to have terrible MUs, especially gatekeepers, so if that's the case, wouldn't she be more of a (low-)mid-tier who has a couple of manageable disadvantages, possibly some advantages, and everything else is "even"?
Brawl Samus's raw frame data if anyone's interested:
http://opensa.dantarion.com/autoframe/FitSamus.php.