I’ve been using Scrivener for a week or so now, and I think you’ve done a fantastic job.
There is one feature I’d like to see added at some point: the addition of a “type” column on the references field. It wouldn’t be a terribly useful feature for Scrivener as it is now; but it would open up a lot of possibilities when/if you add scripting support. For instance:
References between alternative story elements could have types like “conflicts with” and “depends on”. Then a script could recursively trace such references from a selected element, to find the global effect on the rest of the story of using or removing that element.
References between events could have “cause” and “effect” types. A script could then check all the events in a story to make sure they’re in a consistent order.
Characters could reference each other as “mother”, “father”, etc. A script could then use these links to assemble family trees for the characters.
Basically, it would allow scripters to add relational database-like functionality to Scrivener projects without needing particular fields to be hard-coded into the app.