I understand that it would be difficult to come up with a scoring system. I think that if all of us put our heads together that we could come up with some ground rules. Here are some of my thoughts.
Either separate them into leagues and have the eight team leagues only evaluated against other eight team leagues for a top 25 eight team league BCS. Do the same thing with 10, 12 , 14 etc team leagues. Or you make it even out for example if you are in a 14 team conference you get more points than for being in an 8 team league. However the 8 team league will balance itself out because of better players. We could even separate them by scoring systems, keeper, dynasty, and re-draft leagues etc.
Strength of schedule would be an important part as well as roster.
It would be up to each owner to sell his/her team. In Most leagues it's pretty easy to determine the inactivity of owners and the competitiveness of the league. Some leagues that I have seen have 2-3 awesome teams while the other teams suck. The teams in this league would get docked for lack of competitiveness.
I understand the choosing a player for preference. It happens. In my league cris carter has been a team owners favorite player for years. He dropped moss to keep carter 2 years ago. I have like M. Faulk since playing at San Diego St. He will probably be on my team until he retires even if he sucks. That is a choice we make. Could it hurt our scores, ofcourse.
This would also help evaluate everyones team, help owners to know what needs they have, what upgrades they should be focusing on.
These are just some thoughts ofcourse, that is why I am asking everyone what they think. Could be very fun.