I found an old post from last year where I discuss the detriments of the spread 'em out and pass the ball all over the place.
At the end, I discuss how teams need to have more of a balanced attack in order to save their defensive players from being on the filed so much for the season and getting injured come playoff time.
And that the coach that seems to have figured it out was....Jim Harbaugh.
That was when Alex Smith was the QB. And the Grantland article discusses Bill Walsh stating that there is no more innovative running schemes. I saw Harbaugh using innovative running plays last year. Although some of that was just going back to some old running plays like traps and wham blocks.
I just think that the running QB has never really lasted in this game. To win in the NFL, the QB has to beat teams consistently by throwing the ball in the pocket. If you get somebody like Steve Young, who could beat teams from the pocket, then outside the pocket with his arm and if all else fails run with his legs for a first down, you're getting the ideal situation IMO. But, if he's a designed runner, that usually gets figured out sooner or later.