The only reason I got an EX Pass was due to a glitch. Hopefully you'll get a friendly glitch pass someday too.
But honestly, I think they should use Mewtwo to launch the Quest system and swap in a new EX boss. Obviously make Mewtwo's quest challenging but attainable to anyone who puts in the effort.
A couple months ago they said they've only achieved like 10% of their vision for Pokemon Go so hopefully alot of your ideas are in the works