(1) Red underlining wrongly spelled text - if this does exist I can't get it work
Spell and grammar checking is indeed available:
(2) Better layout of info box when selecting "export..." - doesn't feel very mac like
Heh, feedback taken on board. We'll see if we can improve this.
(3) Integrated pandoc? If there is an option for PDF via LATEX, why not expand export via pandoc?
There is an integrated pandoc build actually inside Manuscripts, it's one of the tools we use as part of our exports. What form of pandoc integration would you like to see specifically?
(4) Table of contents layout system
This is an upcoming feature. Right now the live ToC you see as the document outline is the best we can do, and it's great, but indeed we'll also want to allow laying out a ToC as part of the manuscript itself.
(5) Ability to reference sections and subsections within the text
This is indeed an upcoming feature.
CEO & Co-founder of Manuscripts.app Ltd