If you are jailbroken, more options open up, e.g. KOReader.
https://github.com/koreader/koreader/wiki
They don't support taking notes (yet, but I am sure they are working on it).
But they do support highlights, bookmarks, and reading process, all(?) synced to different KOReader instances.
So that works on Kindles and Kobos and Android devices.
There are also instructions for building a KOReader emulator on linux and Windows, but I'm not sure the desktop is on their radar yet (as a supported platform).
Maybe eventually.
They also support Ubuntu Touch, which might offer interesting options re: Ubuntu Desktop Convergence sometime next year, or so they say.