I answered this earlier in the thread but I will explain it again.
... Simply running what we do from the gun isn't really going to work...
For what it's worth, I never said "back the QB up and run the same plays with the same blocking schemes". Would you have to change more than one thing to be successful with a shotgun flexbone? Probably, and I'm not sure how many changes are necessary. There are enough teams running a shotgun flexbone that you don't have to ask whether it's possible, but rather what changes we'd have to make and if we want to make them. Bringing up Army, Navy, and UCF, people have compared strength of schedule; according to the NCAA, our strength of schedule is 25th and most of them are in the 50's and 60's. But F+ factors that in, and ranks all three as better than us this year (
http://www.footballoutsiders.com/stats/fplus). If you say it's just about offense, then FEI ranks Army and UCF way ahead of us and Navy about equal. Either they've got much more talent, or they don't have a major schematic disadvantage.
If you want to do a film school and contrast what we do to what they do, that's fine, but what they're doing is working.
I'm not saying we should change to a shotgun. If you look around at what I've said, that's pretty clear.
When I do talk about offensive changes, I say we should pass both more and more effectively, and I do wonder if our blocking schemes are causing us problems against the Clemson's and Miami's of the world (though maybe it's more us trying to run outside against teams that are way faster than us).
But there are counter-strategies to all the points you're bringing up, and the fact that smart coaches (including some off of CPJ's own coaching tree) are doing things differently speaks to that. I don't think Frost or Niumatalolo or Monken are making those choices out of flashiness or ignorance. I think the main reason that CPJ doesn't make many changes to his offense is because he's been doing it that way for 30 years and sees no reason to change--mainly, that he's dancing with the one who brung him.