There are more readers being developed that accommodate epub3. It is simply a case of taking time to achieve momentum in that direction. Very soon you will see people saying "it doesn't support ePub 3?!?! - what a piece of garbage!"
I know Kris (Marvin developer) is already working on epub3 support and is developing a way to have footnotes/endnotes open in a pop-up. And get this - it would support ePub 2 books without the ePub 3 semantics through some liberal parsing techniques!