In what way has the station transition influenced the story evolvement?

The thread name sums it up.

Additionally, one more specific question:

Have the preconceived LET stories been abandoned, or picked up by Chadwick and the Devs?

Huh? Pardon my ignorance, but uh... What, there's a storyline involved in this game? I thought this was, like, a parallel universe to The Matrix. Like a "What If?" type deal. Like... "What If The Matrix Sucked?"