The exact reason that EVERYONE should get in, seed everyone, top seeds get a bye, 2 games a week.
There are always ways to improve a schedule. Pre-season/in-season tournaments and high level non-region opponents. Even if a school has 14 region games, if you play 2 very strong non-region games and 2 strong tournaments you will have a good strength of schedule. It would encourage some great teams to play the best schedule available instead of putting wins on the schedule.
Upper/lower state finals should be at a neutral site. Basketball already does this, why not soccer????