Today is the fifth Tuesday of the month, which means that my answer to this heartfelt letter is available exclusively to my Patreon patrons.
I suspect that your difficulties with motivation are really at the heart of this. The theory section of the paper is in many ways the place where you sell your work, explaining why it matters to your colleagues and is worth reading. If you're feeling unmotivated or down on yourself, you're going to have a much harder time with that.
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.