No criticism meant here, but do you think that maybe you're expecting too much? Again, not meaning to argue with your analysis, because it makes a lot of sense to me.
I always view this, as the game that wasn't meant to be. In that, the dev only meant to release the initial update, and move on. But people wanted more of the story, and so they continued... Because of that, there was no initial plan or outline for the bigger story. There was no character development or ending beyond the original. I think it is being winged, for the most part.
Because of that, I give it a lot of freedom, and just try to enjoy the crazy ride we're on