re: Somebody explain to me what this Flagship nonsense is

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It's just a term that means the original or first in that university system.

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it means a lot more than that. when funding time comes around and the budget is getting hammered, being the flagship university means you get first shot at needed money. it is everything to the university and what separates it from other universities in the state. it seems as if many, if not most, haven't a clue as to the funding priorities of state entities work.