1. A controller for controlling a multi-variable input system having a plurality of manipulatible variables (MVs) as inputs, and operable to provide a plurality of measurable outputs and at least one unmeasurable output, which unmeasurable output can not be measured in substantially real time and requires external analysis for the determination of parameters thereof, comprising: a system predictive model that provides a model of the dynamics of selected aspects of the operation of the system for modeling the dynamics thereof and providing at least one predicted output for at least a select one of the measurable outputs; an external predictive model for receiving an external analysis of at least one parameter of the unmeasurable output and a desired unmeasurable output value for that at least one parameter, and the external predictive model operable to predict the dynamics of a select one of the measurable outputs as a function of the at least one parameter and the desired unmeasurable output value for the at least one parameter to predict the dynamics as a desired value of the select one of the measurable outputs required to achieve the desired unmeasurable output value; an optimizer for receiving desired values for the selected aspects of the operation of the system modeled by said predictive model and said predicted outputs from said predictive model in addition to the desired value of the select one of the measurable outputs generated by said external predictive model and optimizing the inputs to the predictive model to minimize error between the predicted and desired values; and a control input device for applying the optimized input values to the system after optimization thereof.