Forgive my ignorance, but what are the huge crippling flaws (besides lack of killing ability)? Her roll sucks and her grab is slow as all getup, I guess. At least all of her aerials autocancel.
Lack of killing ability is pretty huge and a pretty big understatement; her killing ability is so bad that every opponent she fights is as survivable as she is, basically negating one of the best things about her. She's also generally very slow and weak with her projectile game (including the tether attack) not being nearly good enough at keeping people out to make up for how much she suffers once they get in. In general, Samus has a lot of mediocre to bad moves as well, meaning in almost every situation she's more limited than the other character (assuming the other character is a highly tiered character). Her completely terrible roll (worst in the game) certainly does her no favors, but she has a lot more fundamental problems. Really, you can just look at the list of "things that are good about Samus", and it's clear it's a lot shorter than the list for most characters. Also, King Dedede gets extra long chaingrabs on her (though only infinite if you are at high damage or poor at grab breaking); that's just another extra problem she has. For super fun trivia, did you know her pummel whiffs on Bowser? Yeah, really; poor Samus.
I don't think I've posted in this topic yet actually.
I really think Wario and Falco are going to be falling in the future. Wario's grab release problems are probably a lot more serious than we've been seeing so far; if people have major problems with him for much longer, they're going to start seeking out whichever character optimally infinites him while not failing at fighting him otherwise and play really defensively just going for the grab in a proper position which they'll then use for multiple minutes as they slowly rack him up to 300% before killing him, totally demoralizing the Wario players as well as getting a really decisive advantage in both clock running and the normal score.
With Falco, can't Pikachu chainthrow him to 90% or something? That's a character ruining flaw, though Falco in general just doesn't seem as good at general combat as the people around him (my perceptions here probably colored by the assumption of a liberal stage list where it's just too easy to put Falco on stages that are awful for him).
To jump to low tiers...
I just can't see Ike below Bowser. Both are generally slow with a lot of bad matchups, but Bowser has more than one "you had better counterpick" matchups (King Dedede and Ice Climbers). Ike has overall a much better spacing game due to his range, and his super jab combo is worth at least as much if not more than the fortress. Bowser does have his grab release shenanigans, but his overall sluggish set of grabs and his inability to force a ground break makes me dubious of those really saving him. Ike also has super armor on a few moves, which is not something Bowser can claim. Even the Bowser boards claim he has losing matchups against the entire top half of the cast and even after 29 matchup discussions have yet to claim an actual positive matchup; when the people you'd expect to overrate Bowser rate him that poorly, you have to wonder.
Ness is just really underrated; I think FOW vs Tyrant did a nice job of supporting my longstanding claim that Ness's overall set of tools are just a lot better than everyone even close to him on this tier list. He has a super good fair (like, almost G&W turtle good), an amazing set of throws including the top tierish bthrow (double points for his great dash grab and on average fastest set of grabs among the entire cast), generally great aerial mobility with five fast and good aerials, all around good range, all around good KO power... His recovery isn't even that bad; he has a fantastic double jump and generally moves quickly enough through the air that people can't physically get over to him to absorb the Pk Thunder before he's sure to make it back, and the way his aerials protect him so well and he maintains full aerial mobility in helpless fall state (unique to him and Lucas) means he's actually amazing at doing high recoveries. He does have the albatross of grab release, but just the list of positives alone is so much longer than what I could dream up for everyone even close to him right now. Ness is poorly represented at tournaments to say the least, but I think it's just a matter of time before it becomes clear to everyone that he needs to move up a lot.
Speaking of longer lists of positives, it's very hard to see Link below Captain Falcon when Link has so many more positives. Sure, his recovery is awful which basically just means poor survivability, but between his amazing projectile game and general disjointedness, Link can actually make himself a threat to good characters at least sometimes. I really don't see Captain Falcon ever doing that unless the person using him is just flat out better than his opponent. The more I've seen this game, I honestly have come to believe that Captain Falcon and Ganondorf need their own tier at the bottom; between the two is debatable, but both just seem a whole lot worse than everyone else with the best evidence being that no one really ever argues that either of them belong in the worst tier while every other character seems a lot more plausible for at least the second to lowest tier. Of course, this low on the tier list tournament data is going to be hard to come by so it's never going to be easy to back up, but from what I've seen out of my region that plays nearly everyone these two really are the biggest stinkers.