Well, right now it is a lose-lose situation for us:
-Either we give up book covers, highlights, annotations and the capability to use Calibre (rename the files with .kepub.epub)
-or we give up all the .kepub features, like the reading statistic, the chapter page numbers on the bottom and the very well working settings (changing line spacing etc. works for epubs that previously did not work) if we keep using epubs.
So, as a conclusion to this, right now I´m not happy with their firmware. But if you guys say that they patched .kepub features to epub features in later versions I have faith left they will someday do it again.