I haven't finished it yet, so this isn't really a spoiler so much as my impressions and what I've heard down the grapevine. I'll tag it anyway.
despite setting up Zelda to have a more active role, the game doesn't really allow her to do that and she is stuck in the castle pretty much the entire time. Everyone constantly reminds Link that he needs to go help her, but she's an afterthought - when you're running around completing side quests and finding things you really don't care about her, or even think about her. When she is shown in flashbacks, she has very little agency, and when she does she is almost solely defined by protecting others by... not doing anything active. It's very trope-y in that regard.
However obviously thatbgame has a range of female characters, many of whom are awesome.
That's a shame, there was a real opportunity here to give her some meaningful agency. I really want a Zelda game that allows you to play both characters, or even flips the roles entirely, I'd hoped this would be a step toward something like that.
As you say the rest of the game does do some good, it's still frustrating though.