Speculation is absolutely part of an excellent experience, but let's not forget:
http://badassdigest.com/2013/06/12/film-crit-hulk-smash-the-age-of-the-convoluted-blockbuster/
I had to head out right after I finished reading this earlier, which is fine because I wanted to spend some time letting it percolate a bit before responding.
I don't disagree with any of his points (apart from his admittedly hesitant praise for Abrams, whom I intensely dislike), but he's discussing film whereas we want to be discussing games. Anything more than the core principles of storytelling can't be universally applied across all mediums. For example, the "Show, don't tell" rule can't really apply to games, where I would argue it needs to be "Play, don't show." Scarlet's story obviously violates that rule, two-levels deep. Not only do we never see Scarlet's origins, we have to read about them outside the established medium entirely.
So when he discusses viewers being kept in the dark, that rule absolutely works for film. But a game is different; the players are an independent part of the world in which the story occurs, and there's a lot of room for them to dig deeper if they want. You can keep the players in the dark on things and have them discover it on their own if they put in the effort or know where to look (I won't even drag in Dulfy on this one, that's a tangent that benefits no one). The problem with Scarlet's story arc is that the mystery just wasn't there to discover until it was almost the end (in this case, I'm talking about stuff like alternative conversations in the Nightmare Tower, plotting the location of the Thumpers, etc.). The whole storyline is plot in the truest sense of the word; things happened, then other things happened, then other things happened, the end. You have to dig outside of the game to find out anything about Scarlet's past, and even then it's still not entirely clear. Meanwhile, we had some interesting characters show up, but did they do anything that stopped Scarlet? It was mostly just twisting about in her wake or cleaning up her messes.
Since we have a week to wait for the Feature Update and because it's a relevant topic, let me ask a question that anybody can feel free to jump in and answer; How would you have handled the "Scarlet" story arc? Specifically in the context that you have to have the same rough bullet points; ley lines, waking a dragon, Lion's Arch and yes, you have to keep Scarlet as the prime mover.
I'll post my idea after I hammer it out a little more (and because this post is already long), but I thought I'd throw it out there now.