Satisfaction comes from sustained tension leading to a climax. The tension in a mystery is usually an unanswered question: who, why, or how.
Nothing gets in your way more than a creative writing degree and a lot of practice doing other kinds of writing, both of which fill your head with all sorts of ideas about what writing should be like.
If you're feeling the urge to go back and fix (or despair over) what you've written already, and if it's getting in the way of powering on toward your goal and your deadline, this post is for you.
The best editors act as therapists and teachers too; like therapy and education, being edited can be emotionally difficult and a challenge to your skills, but if you bring your A-game and ditch your ego, you'll get a whole lot out of it.
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.