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Oh my god, people are dense.
Please find one instance where anyone said Wyoming or New Mexico were superior to a Stanford or Virginia Tech solely based on their "flagship" status while the other school is private or the secondary school in the state.
Flagship is only meaningful in the sense that in UConn's case the state supports the school financially to a great extent academically and athletically, where as some other schools in states may have to share resources or as a private you can't draw from public money. In addition, as the flagship, you're likely who non alumni in the state support athletically as well.
That's it!
I linked below to a statement by a Chancellor expressing the usefulness of the term. Flagship is a useful term in order to differentiate between types of universities. A research university has much costs and expenditures than a non-research school, so the term flagship is used to argue for more support to the state's research oriented institutions over non-research schools.