Ok I'm late to this thread so my requests have no doubt been asked before. Still here we go:
More work on footnotes. The ability to have an un-numbered footnote (= a 'true' footnote) with references in endnotes.
An outliner. The spadework is there already so this shouldn't be too difficult.
Better integration with Bookends.
Indexing and TOC?? Thinking this through I'm not sure these are needed (yet).
Logically there are three main stages in writing a paper.
1 - the outline - getting your ideas in order.
2 - cranking out the words and putting in the references,
3 - layout and production work.
For my money 3 is best done in something like Framemaker, certainly for books (please Adobe

If, when this has been achieved, they want to go for everything bar the kitchen sink in a 'pro' version with more typographical stuff than you can shake a stick at, then good luck to them. Better for the moment to provide what most people want most of the time, and above all, *do it well* and keep it rock solid.
Actually I suspect this is the path Nisus is set on, although with Mellel breathing down their necks they can't afford to stand still. Me, I still prefer NWE - what it does it does well and for the present I can live with its limitations.
Tacitus