I think that part of Emil's problem as a writer is that he writes stories that don't allow for the player to be part of the process. It's Emil's story, we just play it.

Fallout 4 was such a mess because they tried to make the Institute an evil monster and a viable player faction which led to a huge conflict between the stated goals of the Institute and its actual actions. Which wouldn't be so bad if the player could confront them about it but not being able to do so makes the player feel disconnected from the character (in my opinion).

In a TV show that need to respond to player choice doesn't exist which is why it felt more natural. Having other writers on hand didn't hurt either.