Another closed file format. I think we're are in need of a lightweight document format, which is more complex than markdown, but needn't be as complex as docx. A quick google shows some results which look like pet projects of small business which have obviously failed (since I've never heard of them before) All of these new document formats that are pushed by big companies (some are really great I actually love using…
Also, you can export from Paper to Markdown or docx. I've written a few of my github READMEs in Paper and then exported to Markdown and they've worked just fine.
The examples you've mentioned (ctrl-i, ctrl-b, insert hyperlink) all work just fine, as does pasting markdown directly into the editor.
-- I have nothing to do with Dropbox, except as a happy paying customer and a happy Paper user.