No, no, and no.
1) You say real-time physics will improve PA Glitches (whatever those are) and shotgun running will be fixed. First, lets just nip it in the bud when it comes to real-time physics, Madden and NCAA won't have them in this generation of consoles. Say what you want about Backbreaker, the game was bare-bones when compared to NCAA (and Madden). Look at all the features, animations and graphical aspects of the game in comparison to Backbreaker.
Backbreaker sells the Euphoria engine. NCAA sells college football, and everything about it. You think the memory in-game for NCAA could handle the Euphoria engine, along with every feature, pre-game, game mode, and every other small feature in the game?
I doubt EA will take on the Euphoria engine, mainly because they're a top company and they've built on taking chances and making a name for itself. They'll probably have they're own animation engine for the next-gen consoles, and those aren't due for another 2-3 years.
2) The fact that Oregon and the CPU can't run out of the shotgun could be potentially due to a number of reasons we haven't considered.
Maybe it's one of those glitch-type of things where no matter what, Oregon will never be able to run in NCAA games.
More than likely, it has to do with how running plays out of the shotgun are scripted in-game, more so than AI. In real life, running out of the shotgun is the opposite of running out of traditional formations. Where in a typical I-Form, the RB is supposed to hit a designated hole and bounce out if it's possible, running out of the Gun is more based on patience and hitting the open lane when it's there.
Based off of how EA does their plays, all of the run plays are designed for the RB to run outside. So maybe they need to redo the logic on how the OL blocks for running plays out of the gun.
Or, maybe it IS an AI problem. However, EA would have to be careful in making the AI too smart for it's own good. Remember, people thinking individually and independently, and it would be a nightmare if the RB knew where the best hole was each time. I just think they need to somehow redo or re-tune how teams run out of the Gun, because it's ridiculous when you can't even get creative to get a couple yards w/ Oregon on the ground.