This is another one of those things that made an appearance last gen but didn't continue for whatever reason. I like your suggestion for the most part and that's sorta how it was done before. If I'm remembering correctly, you could pick up to ten formations and derivatives of the same formation were counted separately--Ace Twins and Ace Big used up two spots, for example. From there, the plays for each formation were automatically assigned. You couldn't pick the Wishbone and then have 80% of the plays be passing plays. If you picked Wishbone, you got the Wishbone plays and most of them were runs. Now, this was done before team-specific playbooks were introduced so any team that had the Wishbone had the same plays as any other team with the Wishbone. I think I'd be willing to sacrifice the team-specific stuff if they increased the amount of formations that you could pick though.
As for not allowing a playbook with Shotgun formations and the Wishbone, I disagree. Sure, it's not realistic but, at the same time, it's my game and I should be able to play however I want. Maybe they could have certain requirements for playbooks to be used online that would help to enforce that realism but if I want to run both the Shotgun and Wishbone in my offline games, I should be able to.