Those previous years were in pro-style, primarily I-formation offenses. Thus, your statement that those systems inherently produce better rushing is proven incorrect. You just admitted that those pro-style, i-formation systems were hardly the "evidence of quality."
You sure you still want to keep having this conversation at a "system" level?
Our running game has actually been good. Our inabilities have generally been in the passing game-- i.e. Worley's inaccuracy... Worley's trouble knowing his reads... Worley's troubles going through his progressions... WRs running the wrong routes, dropping balls, etc...
Thus, it's more proof that you don't want to install a new system every coupe of years, because you don't want receivers learning new routes every year. You don't want QBs learning new reads and progressions every year... Etc...
It's also due to talent and youth. Maybe you don't like to hear that, but it doesn't change the facts.
To add to your point, can you imagine how much better our average per carry as well as total rush yards would be if teams actually felt the need to respect our passing? these types of things tend to feed on each other.
Edit: Oh yeah.... Not to mention how that impacts down and distance which, if in a positive place, keeps defenses on their heels and guessing all of the time.