I am using now QGIS 2.18, which includes support for GeoPackage format.
I know that GeoPackage is like a replacement for Shapefile but not quite so, as GeoPackage has database capabilities. At same time, GeoPackage isn't a full replacement for SpatiaLite, because it doesn't have spatial queries and functions. Also, Spatialite supports GeoPackage.
So, in the context of QGIS editing, when does it make sense to use GeoPackage (and access GeoPackage from SpatiaLite for Spatial SQL tasks), and when is better to use just Spatialite?