re: Who is the true flagship university in Mississippi?

The term "flagship university" has nothing to do with the quality of a school. It just means it is the center of a university system. For instance, the University of Tennessee is the flagship of the state system of Tennessee, with schools like UT-Chattanooga and UT-Martin as offshoots. In Alabama, the University of Alabama is the flagship with UA-Birmingham and UA-Huntsville as offshoots. So on and so forth.