I think I see what your saying aobut going with the flow. Its well known that walleye eat perch, so stock those two together. There are many examples of this what about channel and blue cats? what is thier optimum forage? Or trout? should trout be stocked with minnows or not?
I think this reasoning is a pretty good basis for stocking decisions but it also runs counter to the principle of fewer species. In nature there is a huge abundance of diffrent forage and predators in each body of water. That is one part of nature everyone agrees we don't want to duplicate.