I use ISE for most of the time for evaluting the tuning of motion systems. Motion system have a motion or target generator that generates a smooth transistion of setpoint from one point to another. A motion system should never have a large error. A good motion system does not make set jumps in the set point.
It seems that process system make step jumps in the set point. In this case the ITAE would be better as it would do a better job of evaluating settling time.
I haven't heard of MVC. I assume you are refering to linear quadratic control or something like that.