The simplest improvement I'd make is to not include inter-subdivision games in subdivision rankings. In the great majority of cases, such games skew the averages positively for the FBS team and negatively for the FCS team. This is unfair to those teams (in both subdivisions) that do not play such games.
See FBS Statistics for rushing, passing, total and scoring offensive and allowed stats. Ordinal rankings are provided for rushing yards, passing yards, total offense and points scored, along with passing efficiency and yards/play. The same average values and rankings are included for the defensive equivalents. FCS Statistics is the same report for FCS teams ignoring games against FBS (or D2, D3 or non-NCAA teams.)
The perpetual question, though, is "How can we tell whether good offensive (defensive) stats are because the team has a good offense (defense) or the opponents have on average bad defenses (offenses)?" One method that can be exploited to resolve that riddle will be the subject of my next essay.