I think Kirk's threesome could've been cut from the film. I think it's a caricature of Kirk to say he would do something like that. I agree with you that Carol's underwear scene is gratuitous. I think showing Zoe's ass was another faux pas. It's not perfect, but the character of Uhura is 10x better than any woman in Starfleet before her. It's just not to where it needs to be outside the Star Trek world.
Kirk's threesome was there to show how immature he was, same with him ogling at Uhura. As for Uhura herself, she's an independent woman who rose through the ranks using her expertise and genius, and you can't really fault her for caring about her boyfriend. For God's sake the man lost almost everything, literally.
Equality isn't numbers here. It's the actions.