I don't believe they were in a good draft position to get a QB his first season as IIRC, that was a weak class for QB's. He also had Vick, who would seem like a perfect fit for the read-option. Then Foles was a 3rd round pick and had a great season (although I think he was lucky a lot of the time). Tough to go after a QB in the first 3 rounds when Foles put up the numbers he did. And not much in the way you can do about backups. Usually if you are using your backup, you're not in a good position to win.
I think the larger issue is that his offense is likely to lead to more QB injuries. Most of the scheme is very basic and part of the key for defenses is to occasionally set up a complex blitz. If the O-Line isn't in position to defend that, it's a free shot on the QB. Also, since you're running more plays, more times the QB can get hit.
YR