Hi Craig, thanks for getting in touch.
I'd love to think that WikiPack would be able to help you with your dissertation! The Markdown engine currently supports tables, but not footnotes yet. Support will be added for them eventually though.
Public pages are definitely on the roadmap, and are an often requested feature. At the moment, I'm aiming to launch soon with two plans, Lite (no dropbox sync), and Personal (Dropbox sync and change history). After that there are a couple of features to roll out, like being able to set a default homepage, and an email inbox. Then the next major update will be publishing pages.
I've had another person ask about custom domains, but haven't looked into it yet. I'm not sure how feasible it is, but if it's possible I'd gladly offer it.
Can't offer an ETA for anything at this stage I'm afraid, but I'm working hard to keep innovating at a good clip.