Dear Piotr,
thank you for an idea. It's seems that finally more and more users know and use the Geopackage format. To be honest we've been thinking about the support of GeoPackage for maybe the last 5 years. I personally prefer this format. But "the problem" is that nobody wants it (with a few exceptions). Most of our users still depend on the SHP format. And because there are more requested or higher priority ideas, we always defer support for GeoPackage. I can not promise when it'll be implemented but it's definitely planned and we'll increase the priority for this task.
Piotr Mędrzycki