Why not?
Why would the creators of the game make it so the characters go in order of "viability"?
If you're going to argue that a skilled ____ player couldn't beat a skilled _____ player, because of a "tier-list" you better have a damn good argument other than that trash.
They don't make bad balance intentionally. For a game as varied as Smash you can't achieve a perfect balance between characters, there will always be characters that have clear advantages over each other, it's quite simple.
For example, Mewtwo in Melee has a very simple design flaw in that he's light-weight (aka easy to kill) but also very tall (not to mention that his tail has a hitbox), which means it's easy to hit him and easy to kill him. On top of that Mewtwo is slow (thus predictable) and has very little KO power, so in the end the only above average thing about him is probably his recovery. We can then compare him to his superior Pokémon counterpart, which is Jigglypuff. She too is light-weight, in fact she has the lowest weight of any Smash Bros character ever, but to make up for it she's small, has a lot of fast and hard-hitting moves in the air, also has a great recovery (5 jumps plus Pound) and she can combo into what is essentially a one-hit KO. While she shares one of the same flaws as Mewtwo she has so many more advantages over him too, thus it's illogical to not say that she's the stronger character.
We can also take a Brawl example. Ganondorf is
very slow and
very predictable and he certainly doesn't hit hard enough to make up for it either, and on top of that he's got a sluggish recovery. Then we have Meta Knight, who is small, fast, has a godly recovery, his attacks out-prioritize everyone else's, he has an unmatched aerial game with incredible gimping potential, he has tons of great tools at his exposal that helps him mix up his approaching abilities (the tornado and gliding being the most notable), and on top of that he has certain attacks that hit just as hard as many of Ganondorf's but comes out a ton faster. The only thing Ganondorf has over Meta Knight at all is his weight, which arguably doesn't matter much considering Meta Knight is a much harder target to hit anyways due to his size and speed.
In the case of Dr. Mario vs Mario in Melee the former hits much harder but has a bit more lag on his moves, while Mario is generally faster but doesn't hit as hard. The trade-off for speed is not considered worth it since Dr. Mario already moves at a decent pace, so he doesn't require said speed as much as Mario requires that extra punch of power.
Fact of the matter is that some characters simple do have better tools and stats than others, perfect balance between characters simply can't be achieved, especially not in a cast of what's currently 48 characters, theoretically a frame-perfect Ganondorf will never be able to beat a frame-perfect Meta Knight in a fair battle because Meta Knight as a whole just has the better stats and moves. Now of course the tier lists aren't necessarily 100% right, they should be read as rough outlines and a general idea of who places where, anyone who takes it too much to heart is going to hurt themselves, there's a reason they change ever so often after all.
's Water Gun, then there'd be no more arguments of who's better or worse, albeit making that "IF" situation is irrelevant.