Well, perhaps this is a little late, but the complaint based on a lack of visible run success with a superior offensive line has been around since Beta. It was one of the more consistent complaints. It was one area where superior numbers never seemed to equal any sort of truly superior advantage. Maybe this has been addressed since Beta. Maybe not. Are you really sure you have been seeing advantages in this area up untill now?
I am not sure comparing stats from players in Beta to players here in live 3.0 with similar attributes always makes sense. Beta filled up with human coaches who signed on for multiple seasons and never finished one. It was common to face teams that had multiple seasons of walkons with no practice plans set. Outside the playoffs, the regular season of Beta was a walkthrough. Sims here and now may very well be tougher than those human and/or humantosim teams in Beta. If there was a "death penalty" in Wis, it is getting a human coach to sign up for multiple seasons and never look at the team. Multiple seasons of walkons sends programs to the darkages, and that was fairly common in Beta, especially at the div 3 level. I remember looking at recruiting and despite having mostly human coaches in the conference I played in, it was almost all walkons for every program outside of Gino's Huntingdon team and my Rowan team. Perhaps each world was different, but I played in the same world as your Christopher Newport team. These programs were nowhere near as good as true sims which presumably is what you are playing against now.
Anyway, sorry you are so frustrated. I won't defend or promote WIS, but customer support did tell me a game guide explaining mechanics is in the works. maybe it is worth sticking around for. Presumably it will have the answers you want.