Digital GPIO vs Analogue inputs on microcontroller
The digital inputs all share the same common ground as the microcontroller.

Not all analog inputs are differential (i.e. having + and - inputs), many microcontrollers allow you to configure them as single-ended or differential for example.  

The differential inputs allow you to be more accurate for very low level signals by rejecting common mode signals and ground errors.  

This is not as necessary for ordinary low speed digital signals as they have the built in noise margin from the logic level specifications.