Today I had a first look at QGIS 2.99 developer/experimental (upcoming 3.0) and big advantages in supporting Geopackage (sometimes called „the new Shapefile“) are made – including editing-support.
QGIS 2.99 allows to create new vector-layers as Geopackage (Layer – Create Layer …) and edit geopackage-layers directly !
I also did a cross-check with ArcGIS Pro (1.3.1) whether geopackage features created by QGIS are smoothly readable by ESRI’s product – YES it is. ESRI supporting geopackage fully (editing !) would be desirable.
PS: Also QGIS 2.16 already supports Geopackage editing.