I agree with the first part of your post (properties, ontologies, namespaces etc.)
Concerning the last part (issues):
- There is indeed much room for improvements in filtering references.
- This is debatable:
- On one hand, it feels familiar to have a built-in way for ad-hoc queries.
- On the other hand, being able to place a query anywhere is very powerful.
- What if simulating the desired feature by:
- Using the right sidebar as a special tab.
- Putting there a dedicated page for all the temporary queries.
- Something like this?