The problem:
The example queries https://quarry.wmflabs.org/query/31002 and https://quarry.wmflabs.org/query/30997 are queries that generate very different result sets, due to the difference in seemingly only 2 SQL joins. The result produced should be broadly the same. It's not straightforward to determine if this is a logical flaw, or a technical issue inside the database itself given the text nature of the query (And this is despite some knowledge of SQL).
I've written a few other queries that get progressively more complex as additional tables are added.
The requested feature:
A way of building queries (possibly visually) , that does not rely on knowing the precise behaviour of the underlying SQL (Such as what exactly is being joined), and where the relationships between the tables can be more easily understood.