I'm going to contest two of your points here:
1) What are you using as a metric of "Successful distance program"? Is developing one of the best steeplers in the nation good or not? He's also had some good success with other athletes, given how long he's been a coach.
Further, why did everyone expect magness to be some wunderkind coach? I mean, he has had some great success, but not sure why he was supposed to be the next great icon in college coaching.
2) I, and many other scientists, don't think altitude is a "huge" advantage. Listed to a former doctoral classmate of Jack Daniels' talk about how they've had difficulty reproducing any benefits to altitude that would be similar to the benefits derived from EPO (which is, as I understand, the primary reason for going to altitude in most people's minds).
Flagstaff does have great scenery, the placebo effect of altitude (if there isn't a true effect), elites (you don't really see them around, or, I haven't), but most importantly, it has a great climate year round, which is the true benefit, I think.