I have the Nexus 6 and have been researching the MTPfailure on Xubuntu 16.04 for about 10 days.
I have Calibre 2.6
After Marshmallow update on my Nexus I find that "Charge Only" is the default setting when USB is connected.
This is documented in the release notes. In order to activate MTP it is necessary to tap the Build Number 7 times. I kid you not.
I have followed
instructions on
Stack Exchange and I cannot discover the Nexus on USB. Therefore cannot transfer books over USB.
My phone also do not have removable SD cards to get around the dastardly restrictions of MTP.
Does Calibre have a recognized alternative for side-loading-- send books to the cloud, download to phone over wireless?