With each update the UI moved piece by piece from library mgmt focus, to shop focus. Personally I wasn't that much annoyed, because I mostly go by filesystem folders, but there are probably some that got shafted.
About the openness of Kobo: my device can dualboot to debian or android in contrast to the Kobo Linux. I was able to change the main storage easily, it was only a microsd card in a slot internally, which after a dd copy to a bigger card was accepted and even recognised as bigger in the UI free space screen. (I'm not talking about the external microsd reader that this device also has.) The battery is a typical lipo flat pack, which should be replacable from some arduino parts online shop.