Again, I've only read the manga so I don't know how they're portrayed in the anime, but:

Yuzuriha: primary purpose is motivation for the male protagonist (ala Miho Asuki in Bakuman)

Kohaku: min-maxed strength and dexterity at the loss of intelligence, wisdom, and self-initiative (and I'm sorry, but that is one ridiculously skimpy outfit, especially given her acrobatic role)

Suika: pre-pubescent characters (thankfully!) usually bypass misogyny/hypersexualization so I don't include her in my assessment

And then there are the other first-half characters, like:

Ruri: helpless sick girl (omg that shot of her being fed medicine)

Kirisame: zero self-initiative (mindlessly follows orders), and that outfit makes Kohaku look like a nun

And a bunch more that I don't remember because it's been a while since I read the series.

The first female character I didn't feel at least a little uncomfortable about was Chelsea, who I think is actually a strong character and the first (non-child) female character to be accepted into the group for her insight, smarts, and decision-making skills, AND her design is not sexualized (almost as if she stumbled in from another series). But she appears quite late in the series, hence my comment about the first half. Some of the American female characters are also okay, but not great (and again, introduced in the latter half). But even towards the end, the male characters are in nearly all the leadership positions, and the female characters are left to play support.

I don't mean to single out Dr Stone; you could do a similar analysis for most anime and nearly all shonen series. But especially given the gender imbalance in STEM, it's unfortunate to see more business as usual.