Samus's sex has been exploited from the beginning. This is something I will neither deny, nor attempt to defend. The fastest time depictions of her have typically shown her in skimpy clothes striking a sexy pose, with little or no context, like she was a Barbie doll tossed in for male amusement. Despite all that, I can still argue that some appreciation needs to be given for the fact Samus being a woman at all was really subversive and cool given the time period. It was such a momentous step forward for one of gaming's most consummate badasses to be a woman, that for her to show up in skimpy outfits could be forgiven, hell, even embraced, given appropriate context; maybe the climate on her home planet is very hot, maybe she just likes wearing those clothes. It's not even really inherently wrong for a woman to wear clothes that show a bunch of skin. You just have to have a good answer to the question, "why."
Back in the day, it was really hard to provide an adequate answer to that question. But now it's not. Games have tremendous storytelling power now. It's possible to show Samus in a casual setting, and provide hints of context. If we see a bunch of other humans around wearing similarly small clothing, then we know that's just a fashionable thing, and that can be the end of it. I personally would think post-Fusion, Samus would be seen in warm clothes, given her new sensitivity to cold, but that's just speculation.
Another thing that's changed is that some gamers are aware now of social issues, and many are starting to point out the objectification of women in games, and serving a vital role of at least broaching the question, "why?" What's really upsetting about Samus's portrayal, is that in attempting to answer that question, Nintendo has either made it worse, or brought in a whole new wave of situations where "why" must be asked. The introduction of high heels is a great place to ask the question, "why," and demand not just a half-assed answer, but an answer that makes sense, and doesn't lead to another "why."
Why does ZSS have high heels now? The popular answer is that heels hurt more. I don't think this answer is adequate. Samus could already do this in nothing but a jumpsuit at age sixteen:
It stands to reason a kick from someone like this would be lethal barefoot. So why are the heels so necessary as to outweigh their impracticality? Well, on their own, they're really not. If she needs the extra durability, she's got a friggin' power suit anyway. The jet boots add another attempt to answer why. "Well, they need to have a place for the jet fuselage!" I don't know how much I agree here. I mean, does Iron Man wear heels for his repulsors? No. This is a purely fictional technology we're supposing here, so the explanation for its appearance is just rationalization. That means you're just rationalizing to answer why ZSS is now wearing high heels, and a rationalization is still not an adequate answer to the question, "why."
So I always answer the question of why I dislike the heels with another question. Why does she have them?