Teams stopped us in 2013 the same way, where they would simply drop 8 in a short zone coverage.
With no arm strength from Tommy Rees, and no running threat from the quarterback, it made things much simpler for opposing defenses. The only things that kept us from having a disastrous year were that Rees was easily one of the best at making pass protection audibles, that the running backs were pretty good at pass blocking / route running, and that this would buy Rees enough time for a receiver to finally get open.
We were quite capable of running in 2013 (Atkinson was averaging 6 yards a carry, McDaniel at 4.6, Folston at 5.3, and Carlisle at 4.3). We simply chose not to do so, which made it even easier for the defenses.
That being said, I do credit Brian Kelly for being able to squeeze out every last drop of performance from Tommy Rees that year. That 9 win season was about as good as we could have hoped to have, and was probably the one of the best examples of his ability to coach a team (2012, 2015, and arguably, 2017 were the only other good or excellent seasons).