Problem with Generic Formulation

As it stands the Generic MDP Formulation in Matlab script is exceedingly slow. Even with some speed ups, it took about 12000 sec ~ 3.3 hours to compile to statistics for the New Graph. I learned from some Matlab forums that vectorization is the key to speedy Matlab scripts. Currently most of my major data structures are matrices, chosen for the ease of debugging readability. However with larger problems come larger data matrices that will be too large to display in Matlab. I might be better off vectorizing everything.