1) The main advantage is that can set outputs with more than just % vbus.ie you can actually set outputs in terms of absolute voltage and current. You can also set speed/position commands, and assuming the encoders/pots are wired to the jaguar correctly and the PID is tuned correctly, the Jag will handle the control loop for it's motor automatically (and probably w/ a lower dt than the cRio)
2) No, it won't.
3) Probably by sending data over a UDP port. (not 100% sure since my team hasn't attempted this, also not sure about implementation semantics).
5) Either UDP, or have the raspPi output PWM using it's GPIO (or an actual analog signal using the audio port) and treat it like any other digital/analog signal. (You can also try I2C or SPI)
For anything related to jaguars, you should probably first read the
documentation on it for more detailed answers.