The playoff system will not make anything fair and it will not silence critics, it will only make more money for the gaming industry. No matter what the system, no matter what the decision and no matter what the outcome, there will be a fanbase or a conference bitching and moaning that their team(s) got hosed.
The only way to make a true championship is an 8 team playoff against the 6 strongest conferences and 2 at large. Then you will have a real champion like every other sport.