Hi to All, I have already solved and tested this issue on Armbian build. Find patches for both legacy (3.4.111) and mainline (4.5.2) kernels on: http://forum.armbian.com/index.php/topic/853-armbian-customization/page-2#entry7494 There it is also described how to do eMMC bootable and much more.
About the board - Olimex already sold all 3 kinds after migration to their HW rev. E. One have to specify Lime2-eMMC as A20-Olinuxino-Lime2-eMMC instead of their old 2 options A20-Olinuxino-Lime2(-4GB). Regards Chris