I prefer the GeoPackage format [1]. Very similar to SpatiaLite it is based on SQLite, but as official OGC standard I anticipate better integration and support in the long run.
https://www.geopackage.org/implementations.html
https://www.gaia-gis.it/fossil/libspatialite/wiki?name=4.2.0...
See the extensive list of spatial query operators here: http://www.gaia-gis.it/gaia-sins/spatialite-sql-4.2.0.html