Blue Dot allows you to control your Raspberry Pi projects wirelessly - it's a Bluetooth remote and zero boiler plate Python library. Makes it easy to use Bluetooth. Has excellent documentation, including how to pair your RasPi with your phone from the command line. Seems to work pretty well. Bluetooth interface is only up while BlueDot.wait_for_press() is running. Has a serial communications API, also, for sending and receiving arbitrary data.
I don't see why this module couldn't be used more generically to interact with arbitrary Linux boxen over arbitrary Bluetooth interfaces. HCI is HCI, right?
The matching Android app is in the Play store. There is even a version of the Bluedot app written in Python that you can use from the desktop to interact over Bluetooth.
Requires that the dbus-python module be installed to the same venv. Also requires that the shell running the Python interpreter have sufficient access privileges to interact with the Bluetooth interface (root certainly works), usually the bluetooth group.