This seems like an unnecessarily negative comment. I've been a user of SQLite for over 20 years now (time flies!), what you're calling lack of polish, I would chalk up to Dr. Hipp has been consciousness about maintaining compatibility over the long term. So much so, that the Library of Congress recommends it for long-term preservation of data.
Long term compatibility (i.e. prioritizing the needs of users vs chasing inevitably changing ideas about what feels polished or pristine), near fanatical dedication to testing and quality, and sustained improvement over decades - these are the actual signs of true craftsmanship in an engineering project.
(plus, I don't agree with you that the storage layer, column format, or SQL implementation are bad).