After discussing this question offline with Nicholas, we identified that the fitting of convex hull boundary models was taking a very long time with large data sets and number of inputs. Fitting a convex hull boundary model occurs by default from R2014b. You can uncheck the Fit boundary model option in the Fit Models dialog or wizard.
In R2015b we changed the default boundary model to be pairwise convex hulls when there are more than 10 inputs or more than 2000 data points. The R2015b release notes provide details.