I switch between using yWriter and Scrivener for similar reasons.
I think it’s worth pointing out that yWriter is a basic editor hooked into a meta-data tracking system, while Scrivener is a tool focused on the process of writing formal &/or long documents. Meta-data tracking that is too specialized adds complexity while only helping a subset of users.
However, as we have a “templates” folder, I could imagine having an “in-line references” folder or something like that, with a toggle-able option to automatically create document links based on the document names in that folder. Then it wouldn’t limit the usefulness to just characters / locations / items, as is the case with yWriter.
Something that might be a “next-step” would be reciprocal links appended to the bottom of the linked documents.
That’s just my two cents, though.