Self-criticism is incredibly painful, because we know where all our own weak spots are. But by that same logic, we can also be our own best allies, cheerleaders, and friends.
It sounds like going scene by scene and character by character has been helpful for you to this point, but it's not what you need right now. You need to see the novel as a novel, to grasp it in its entirety and understand not just the individual parts but how they all work together. You need to turn off your engineering brain and get the book's gestalt. And how you do that is: you read the book.
Books often change quite a lot as you're writing them and the book you've written may require a somewhat different protagonist than was called for in your original outline.
If no one reads your stories about queer girls in space, that's not a judgment on you. And if everyone loves your stories about queer girls in space, that's not a judgment on you. The work is the work.
Today is the fifth Tuesday of the month, which means that my answer to this heartfelt letter is available exclusively to my Patreon patrons.
Being a doormat is not something readers generally find appealing in any character, and particularly in a main character. Give her things to do and let her do them. Let her take risks and sometimes succeed and sometimes fail. Let her pick a goal and commit to it and pursue it. Let her, as you say, make choices. Otherwise she isn't really a character; she's exposition with a face and a name.
Book middles frequently involve beloved characters being in serious peril or coming to harm, a proliferation of plot threads that can feel out of control, or a mess of problems with no apparent solution. These are things that can be genuinely hard for writers to face, just as they're hard for characters to face. It's so much easier and more enjoyable to focus on the beginning, when everything's fun and exciting, and the end, when all the questions are answered.
When you're wrestling with yourself, it's very easy to wind up in a stalemate, also known as being blocked or stuck. You don't want to give up on the project, because it means a lot to you. But you don't want to proceed, because it's painful and difficult and also maybe because you're mad at yourself for setting yourself a painful difficult task. So you sit there and look at those ten pages and wonder what's wrong.