Well.
Act 3 needs a complete overhaul. The main story needs rewrites here and there, which are completely doable btw if they intended to release a definitive edition next year. Now you already have the framework. And millions of players playtesting.. Like stated above I think if you sum up the story it sounds like an incredible premise for a story. Unfortunately the plot does not come together, but drifts apart.
I don' t agree that the plot is bad from the onset, I do agree that it rapidly starts becoming more frustrating with the reveal of the Emperor.