Formation IQ also comes into play more now in version 3.1, so having to play young players with low formation IQ will also lead to lower overall performance.
Pete_61 was kind enough to spend some time with me on the basics of building a roster when I returned to the game and FIQ was a point of emphasis. Although the logic of the above statement is self-evident when you think about it, I did not place very much emphasis on FIQ (except for QB) until after my discussion. Since I started paying attention, my penalties have gone way down and I have been able to sustain longer drives. Penalties are drive killers (at least for me).
So...good depth means that you have more experienced players in your rotation which means you do not have a severe drop in FIQ at any given time. For me, this is the main reason to have depth especially on the lines.