Some spoiler thoughts on the overall game/story now that I've finished it.
The episodic structure was probably a mistake. In retrospect, it feels like the story doesn't really get going until episode 3 or 4, especially for Zoe.
I didn't have any major issues with where the story went and I was mostly satisfied with the resolution of all the hanging threads from Dreamfall. The one real sticking point I had, predictably, was Saga and her role in the story. I didn't mind the character, but for someone we spend a LOT of time with over the course of the game, we end up finding out nothing about who her parents are, where her powers come from, where this very specific prophecy about Kian came from, and how she ended up tasked with fulfilling it. Pretty much all of her development that actually relates to the larger story, takes place offscreen between episodes 4 and 5.
Loved the voice performances throughout. Zoe and Kian were both outstanding, and it's always a treat to hear Dave Fennoy even though the character he played was a bit of a turd IMO.
Also, after spending this entire saga preventing the unification of Stark and Arcadia, you find out, through an optional prompt in the epilogue, that they eventually end up unifying anyway?? That seems like kind of a big deal. Maybe this was what The Longest Journey Home would have been about?
Pretty much agree with everything you said. There's definitely some great aspects to the game but some notable flaws/some confusing story issues that mar the experience bit. Still, I think it was worth playing, especially for fans of the series.