OK, let's get some things straight on this topic.
1. Boone is not all that different from Flagstaff in terms of the town's "feel." It is a realatively small town that is dominated by the university that's there. It has some tourist appeal, as does Flag, and it's got that "mountain vibe" going that draws in the granolas and artisans. It is definitely smaller than Flagstaff, but the two really aren't that different.
2. Boone's weather isn't nearly as good as Flag. It is hotter in the summer, and as cold or colder in the winter - and without the sunny days that Flag still gets. It is a "wet cold" and "stuffy heat" kind of climate, but the summers are mild enough that the App State dorms lack AC.
3. The trails/routes in Boone are probably better than those in Flagstaff, especially if you work in the general area. They tend to be more for general pedestrian use (ie, old people and tourists) and I think this is better for running as they're wider and smoother than say the trails on the Peaks and such.
4. Altitude in Boone is a non-factor and should not be considered as a reason for coming. The mountains in Boone top out much lower than is needed for real benefit - it's not really even that much higher than say Atlanta or Ashville. Those who say they use Boone for "altitude" have never really done time at 7,000+.
5. 13:30-14:30 is not Elite. Heck, it's barely All-American. That said, there are a lot of people who choose Boone specifically to train, so there are plenty of runners around.
All in all, I'd give Boone the edge in running routes and probably training partners. Flag in everything else.