Another factor is DRM. We may not like DRM, Kobo may or may not like DRM, but the publishers seem to love it. DRM is kinda hard to enforce when someone can modify the code to circumvent it, modify the code to dump encryption keys to disk, etc..

Besides, the quality of the software depends mostly upon the people maintaining it. Open source software does well when there is strong leadership and talented developers. Proprietary software does well when there is strong leadership and talented developers. Because of this, we see excellent software on both sides of the fence. In other words, don't expect open source to be some sort of pancea.