Great topic here, I'll take a shot....
I think the playoff system is good with 16 teams but how they get there needs help. My suggestion is to reseed the teams once the power points are added up. Use an objective committee or computer program to consider the obvious-like beating a AAAA Pub team is not the same as beating a SOL National team even if the records are the same. Look at teams strength of schedule especially in their wins.
My most important change is spending $20 million on a plot of land that is setup for football, soccer, field hockey, lacrosse, baseball, and track. Have multiple facilities and fields for use as Championship sites. The football stadium would seat 15,000, great press box area, plenty of parking, luxury suites for sponsors, and be a FOOTBALL ONLY field. This would eliminate any doubt where the Final is played every year. Hopefully, there is land available near Ft. Washington or Western Montco so its centrally located.
I think KBerg suggested playing an inter conference non-league weekend, I say go the other way. Schedule a District 11 or District 3 vs. District 1 Challenge. Give fans from other areas a chance to see teams they only read about. Play 4 games on Friday and 4 games on Saturday the weekend before Labor Day. Imagine a Wk 1 lineup of Pennsbury vs. Central Dauphin, or North Penn vs. Parkland, or Coatesville vs. Easton all played at a venue in each District. Maybe Lehigh for D11, Hershey for D3, PPL for District 1.