I'm with you. I've encountered numerous situations where the query planner caused issues. I don't know if the alternatives are better, but it's definitely an issue. I've written multiple databases wrapping SQLite, and multiple bindings to SQLite. There are dragons.
I had to use sqlite once for something that would do a ton of read queries on a particular table. Sometimes just swapping the order of operands to an and operation generated a completely different query plan. Had to scour their optimizer document and painstakingly check the query plans of, and then manually tune, each sql statement.
