I'm only an hour into Frame Trap (and up to Chapter 10 in FFXV...) but this is a fantastic discussion. Ben, have you played Type-0? Because FFXV has the EXACT same problems I had with that game. It doesn't explain anything. You're thrown into the game with a cast of characters and you have no idea who they are or what their backstory is. How do you find this out, you ask? By reading the f'n manga that was only available as part of the CE.
It was one of the things I was most concerned about going into FFXV and based on what I've played so far, I think that while Tabata makes really fun games, he's a terrible story teller. Not one of his games has had even a decent story, they're vague, incoherent messes. People give Toriyama and Nomura a lot of flack but at least you can actually follow their dumb, convoluted stories.
I really think Square Enix would be best served ripping off Naughty Dog's development structure. Instead of just having one guy direct the entire game, they need a Creative Director in charge of the narrative and performances (who can, you know, actually tell a good story) and a Game Director in charge of the game design.