Your alternative is... what exactly? A unique and baroque file format for each application (see: Git)? Folders of JSON or markdown files which are slow, easily corrupted, and lack indexing? Depend on some memory-heavy external DB service like Postgres?
In most cases, embedding SQLite is the best solution. And that is exactly what it was designed for.
In most cases, embedding SQLite is the best solution. And that is exactly what it was designed for.