Although we can never be sure, I guess we can still speculate this. From what I gather, the Chapter 5 Helena Chang and the Vagabond part was written during 2007. Same thing goes for Saga, Brian Westhouse, and Roper Klacks I guess.
But I feel like Yaga and the Lux are recent additions to the storyline. I am still not sure who was the Sky God, and why it was searching for Zoe?
Also it was said that the Dragons were quite important to the storyline, yet we still haven't met a single one. ( There still some speculation about Queenie, but that is a topic for another day.)
I have a feeling that there is a whole book on abandoned story arcs for Dreamfall chapters, but I guess that is a discussion for another day.