@adriano in one episode Batō suggests that Motoko should just switch to a male body type, since she acts like a man already (I think this is a jab not just at her general stoicism, but at the fact that she's shown to have a history of lesbian lovers). in response, she pulls Batō into a fight and destabilises him with a smile, then applies some judou to let him fall onto his own weight. "I can redirect the power of idiots better with a female body", she says triumphantly.
speaking from the point of view of a trans woman I find Kusanagi Motoko gives a much better portrayal of the joy of a woman body. her use of sexy outfits feels intentional. with Quiet being literally muted, she feels way more of an object for the male gaze than the Major. the excuse given for her skimpy outfits robs her of agency (she doesn't revel in looking sexy, she *has* to expose her skin) and feels unconvincing, because if it's all about exposing skin to sunlight, why does she dress sexy? sexy is not the same as maximum exposure. if I was a combatant with Quiet's condition I would wear tactical shorts full of pockets and a sports bra, not ripped thighs and a shiny bikini.
this also comes off on their personalities, with Quiet being childlike and impulse, while Motoko is maybe the most logical and cold of Section 9. she just feels like she's drawn by Masamune as his ideal of woman to admire, while Quiet is written like a fantasy of a woman to own.