As far as Samus goes, I have been really surprised how much perception of her has shifted. A little over a year ago, every thread I went into I would argue with people that Samus wasn't bottom 3/5. Now the majority of people, even new users in the Community Voted Tier List who I used to consider notorious for putting Samus dead last, are putting Samus as mid tier.
At this point, I have no clue where Samus should land. Her viability doesn't hinge on certain character archetypes, for instance. Rushdown, swordies, and zoners don't strictly beat Samus just because of their playstyles. This is because Samus does respectably well in CQC and long range (specifically preventing others from playing long range), and does very well at mid range. Her position in the game hinges more on odd characteristics like opponent hurtbox size or whether they have items that clank with CS.
It's really cliche and everyone has heard it before, but a player has to put a lot of time into Samus to be able to accurately place her or understand her. This is because Samus is a character with depth, and Samus is a character that new players will make bad decisions with because they view her moveset incorrectly or are used to doing something with another character. It isn't even necessarily whether or not the player is new to Samus, it's if they can understand what is good and what isn't. Many new Samus players use SH fair. Many older Samus players also use SH fair because they never broke the habit. Esam uses it all the time. Even JWest uses it. Other Samus players look at down b and think, "Wow, that move is good for landing," and use down b every time they are in the air and die every time. JWest loses stocks to Sheik players because he always uses down b, then gets uaired by Sheik. These are just two examples, but players who consistently do this will probably have their opinion affected by thinking, "Samus has a bad neutral," and, "Samus can't land." There's also the issue of players not knowing how to shad, so they roll and never bother learning shad.
Samus has a ton of room to grow. Her tech chase setups are known, but extremely unexplored. All we know at this point is stuff like fuzzy percent ranges for moves that setup tech chases, but not which characters can jump at which percents, etc. The other thing is that Samus' tech chase setup moves mostly come from midrange, and many Samus players still do not play midrange, and her midrange game in general is hard to master. If Samus' various tools like her midrange game, tech chase CS, and zair combos are fully optimized, I could see her going far. Samus' advantage state is already ridiculous, but it could be improved even more.
This is sort of random, but god I love Samus' up b. Fast oos, covers so many ledge options, does massive shield damage, has some invincibility, isn't too easy to contest off stage, and kills. It lets Samus camp platforms since up b oos kills so early from high up, and when opponents mess up a combo, Samus can catch them in the air with up b and kill them early. Prevents shield bullying, and covers the air above Samus at unreactable speeds since it jumps from the ground to full height so fast.
I think most people pretty much know Samus' main issues. I would say Samus' initial poor reception was a result of her flaws being much more visible than her strengths. It's much easier for someone to see that she has a bad grab and struggles with small characters than it is to see that she has a good, say, falling uair. After a while people started looking for reasons to justify her being bottom tier and made up stuff like CS being a bad move or her recovery being one of the worst in the game, perceptions that still have to be broken occasionally.
In the end, what makes Samus' situation so unclear is how much her flaws really hold her back. Samus has a good moveset, adaptability, mobility (with her aerial acceleration, jumpsquat, and burst options, in addition to decent speed stats), damage racking, kill power, ledge options, and weight, among other things, but a poor grab, roll, jab (depending on percent range), hurtbox size, landing options, and issues with small opponents.
Samus is a character with many strong advantages, but some issues, so it comes down to, "Are her weaknesses great enough relative to her strengths to hold her back significantly?" The answer will vary a lot based on who is answering. But something to keep in mind is, is the person answering that question someone who knows Samus? In Mr. R's case, for instance, I highly doubt it. Results right now say no, her strengths outweigh her weaknesses, many players say that. But in the long run, we don't really know how detrimental Samus' weaknesses are, and that makes her position very unclear.