A few things:
1) It's okay for characters to have weaknesses, geez. When looking at how characters are patched, I always see the suggestions being "Remove their weak points! They aggravate me and I wish they'd go away!" Like, I know that having a character's weaknesses exploited feels so awful when you're on the receiving end, but it's better than evening them out and homogenizing characters.
Mewtwo, for example, while yeah I'd love it if they did things like put on more invincibility for his rolls and such (did anyone check to see if ledge getup isn't so terrible anymore?), I think the Down Smash and Forward Throw buffs work so well in line with the type of character Mewtwo is supposed to be, which is that glass cannon. Down Smash kills significantly earlier now, and is a threat to characters who are both either light or floaty because the angle it sends you away. It's basically a slightly worse Meta Knight F-Smash. Forward Throw is now I think the strongest throw in the game in terms of damage. Those sorts of small numbers add up. I think any Mewtwo player is aware of the fact that often times if the first up throw doesn't get 'em, the second one will, and being able to tack on an extra 3% here and there adds up over time.
2) Samus might be low tier or whatever, but pointing out all of the weaknesses of her "missing" hitboxes feels a bit disingenuous, because a lot of those attacks are still really good.
Dash Attack moves Samus way the hell forward, does decent damage, leads into combos and followups. Sure, it doesn't hit up close, but both Falcon and Meta Knight have dash grabs that whiff at close range, and I don't think anyone considers those bad dash grabs, just the opposite. It's a bit apples and oranges because it's a dash attack vs. a grab, but having a dash attack move you forward that much is a good thing, even if it's not ideal.
Oh no, Samus grabs aren't kill moves. This might sound strange coming from a Mewtwo but why are people so obsessed with every character having incredible throws, whether it's Marth "needing" combo throws or Samus's lack of kill throws? "All" she can do is rapid pummel (thus reducing staling on her stronger moves), and still throw them off stage and force them to confront a charge shot, which now after all of those pummels is either likely fresh or close to it. It's still a tether, of course, but hey.
Speaking of kill moves, I don't think Samus is lacking them in any way either. A Frame 10 F-Smash that kills fairly early when sweetspotted? Screw Attack? Up Tilt? Down Tilt? CHARGE SHOT? Let's also keep in mind that Samus is HEAVY and so gets rage built up onto her fairly easily. Coming from Mega Man, knowing how rage affects your moves is especially vital, because as he takes more damage the number of kill moves he has increases. While I'm not certain on this, I do wonder if Samus is also affected by this.
I think overall Samus is not meant to be a "reliable" character in the sense that option A naturally flows into option B. Almost everything you have to do is based on trying to pick the right choice in context rather than there being a right choice in general. Jab 1 doesn't link into Jab 2, but you can Jab once and then go for something else, and when they start to counter whatever else you're doing, that's when you Jab 2. She has the tools to fight at close and long range, and you have to choose which is the right choice in any given situation.
3) Falco does make sense as a character, it's just that his past incarnations have often skewed him away from what he was supposed to be. Losing dair hurts, and that's something i perhaps don't agree with, but if you look at how Falco is set up in Smash 4, he's basically meant to not really approach from a long distance. Short hop lasers are out, run speed is bad.
However, lasers in general prevent the opponent from trying to get too much distance from Falco. They force approaches, and are good for tacking on bits of damage if the opponent tries to break away. If they try to fight a projectile war, why look, there's a reflector that's ALSO A TRANSCENDENT PROJECTILE. Run speed is bad, but walk speed is great. So basically, Falco is designed to force approaches into close range where his neutral and footsies are well above average. Falco draws you into him, into the area where he excels. The results didn't quite live up to the design a few patches ago, but tiny, tiny changes have made such a difference. If his game plan wasn't clear before, I think it certainly is now, and the only thing preventing people from seeing that is "wah, where's my laser canceling, wah, where's my instant spike?"