Sort of superseded in the GIS world by the geopackage (https://www.geopackage.org/): another spatial standard built with SQLite databases. Geopackages are less about manipulation/analysis at the sql level and more about storage—the idea is you’re already using something like QGIS that can perform analysis
If by "they" you mean spatialite and geopackage then they are very much comparable, in that they are both ways to store spatial data in sqlite databases.
From the geopackage FAQs[0]:
> What is the relationship between GeoPackage and SpatiaLite?
>
> SpatiaLite was a major influence on the vector portions of GeoPackage but after extensive
> discussions, the working group chose to diverge from the SpatiaLite format in a few subtle ways.
> SpatiaLite now supports GeoPackage as of version 4.2.0.
Sure, but Geopackage is a transport format: it describes itself as "a format for transferring geospatial information".
Spatialite is a spatial analysis database: it describes itself as "a complete and powerful Spatial DBMS (mostly OGC-SFS compliant".
They both use the same container, SQLite. And indeed there are other geospatial formats built on SQLite, such as mbtiles. But the intents are very different.
