If I were a betting kind of gal, my bet would be that font handling is one thing we will be seeing a change in sooner rather than later. I installed Gentium Book to see what folks were talking about. It looks awful in ePUB, much, much better in kepub.
That kind of thing used to happen from time to time in the past--the kepub advantage. The developers did come through for us with changes that equalized this kind of thing, but it wasn't always as fast as anyone (including me) wanted.
I have not experienced degradation with built in fonts, though I have done some fine tuning.
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