Flagships come in different sizes. Here are some examples of smaller flagships with excellent reputations in bigger towns or cities (undergraduate enrollment in parentheses):
SUNY Binghamton (14,700)
University of Delaware (19,300)
University of Pittsburgh (20,400)
University of North Carolina (21,100)
University of Vermont (12,300)
University of Virginia (17,900)
Bonus Pick: Miami University (Ohio) [16,800] - not a flagship, but just as good