Then how? They should have at least kept them a lot closer to each other in terms of how good they are, but instead made it even worse (ZSS now has less problems with recovery and KOing as far as i know and Samus has a lot of things nerfed, most importantly missiles since now they have landing lag).
I mean characters are not deliberately designed to be "better" or "poorer". Magikarp could very well be high-tier while Gyarados could be low-tier and it wouldn't make a lick of difference to their "accurate portrayal".
Y'know why?
'Cos certain character types benefit in this style of game. Fast, agile characters with decent recoveries and strong attacks are naturally going to dominate the upper tiers, whereas slower and heavier characters aren't as naturally adept at getting the good stuff.
Does that make high-tiers objectively better, or low-tiers totally unplayable? Of course not. It just means you've gotta put effort into mitigating their weaknesses, while the faster fighters can just swoop in and unleash hell as they see fit. So to use your example, if Magikarp was faster and safer in every way than Gyarados, he'd probably end up on a higher tier. That doesn't mean it's not an "accurate portrayal", it just means one style is naturally safer to play than the other.
Same with Samus and ZSS. Samus is slow and heavy, while ZSS is quick and lithe. ZSS also has a lot of potent combos and relatively safe KO options compared to Samus, so it's natural that she's widely regarded as the "superior" Samus. And as I recall, ZSS was actually nerfed heavily between the E3 invitational and the final release.
That said, as Frostwraith mentioned, tiers are a fan-made concept. They don't exist in the developers' schematics, they just happen based on aggregate results and detailed study.
Smash 4 is a
lot more balanced than previous Smash games, insofar as any character can potentially take on any other and expect to do well, provided the player is sufficiently skilled and knowledgeable of the matchup. Just because ZSS is regarded as a safer and easier to play character, and hence played a lot and known to get good results, does not mean she is objectively better than Samus or that it's going against canon. The important thing is capturing the spirit of the character and ensuring they're relatively balanced: making ZSS objectively weaker than and, overall, inferior to Samus would be just as egregious as making the former better than the latter.