The first thing is that we will have a choice of using Java next year. See
http://sunspotworld.com/frc/Welcome.html.
The second is that somewhere in the future, the CAN bus will be opened to us on the Jaguars. There is a PID controller in the Jaguar that can be used to control position or speed of the motor, plugging a potentiometer or quadrature encoder directly into the jaguar. It can also use voltage control directly, similar to the pwm signal we have now, or a current control to provide a constant torque with the motor.
We will also be able to read the current going to the motors as well as the temperature of the Jaguars through the CAN bus.