Flagstaff is beautiful and vibrant. Not much else, really. I don’t go to NAU (I go to community college less than a mile away), but my girlfriend attends. Almost from the first day, she wanted to transfer, mostly because she feels that the school isn’t intellectually stimulating enough. If you’re looking for a big party scene, come to Flagstaff. If you’re looking for a good school, go to U of A. Like I said, this is mostly based on what friends at both schools have told me.
But, yes, I’d say that Flagstaff is a much better college town than Tucson. Tucson is pretty…blah.