Your ad with marco.org worked, I had never heard about you, but found you there. I have been more than average interested in academic writing and tools for academics for a long time. I'm a PhD student in education, in the final phases of writing my dissertation. I spent a bunch of time exploring an integrated way of managing bibliography and taking notes, and also helped organize a hackathon/meetup around Markdown for science. Also have tried using Emacs and Orgmode, etc.
Currently, I'm using my hacked up system for keeping bibliography, and write everything in Scrivener, however I just write it in plain text, with pandoc-like citations, and then use Pandoc to turn it into a Word file, and process the citations. This Word file is then shared with my advisor, and from there, it's all done in Word (because of track changes etc).
I could absolutely see myself loving Manuscripts.app - I love the idea of being able to import Markdown and have it reflected in the outline, better integration of citations, export formats, styles etc. It makes so much sense. However, there are a few show-stoppers. First of all, it seems quite buggy, I managed to crash it a number of times within minutes of installing it. I tried importing a Markdown file (that I was working on), and it crashed upon parsing it. The second time, it did work, and it was amazing to see my Markdown headers turned into an outline!
Then I tried a few other things, and it crashed two times more. (I reported to Apple each time, not sure if those reports go to you as well).
But other than instability (which is a major showstopper, even if you have continuous saving - when you're in the middle of writing you really need stability), the lack of split-screen was the major showstopper. This is my absolute favorite feature in Scrivener, and I cannot work without it.
Also being able to separate Research from Document stuff, but keep it all in the same file, is amazing. Being able to have all my notes about the different sections, which I keep open in a split window, while I'm actually writing the section in the other split window... Great.
If you put that in, and fixed the crashes, I'd be willing to give it a serious try to see if it could replace Scrivener for me. Now if you got a good story for collaborative editing (I don't need live concurrent, just ability to mail diffs back and forth with track changes and comments, approving or not changes, etc - however you implement it), this would be a complete game changer! My supervisor is not a luddite, and he might be willing to try something like this if it was easy and streamlined. And it would make my life so much easier!
Anyway I wrote this much because I really believe in your product and idea and I would love to see it succeed!