I'd blame it on Sawyer but... I can't. The problems with the game aren't entirely the system. The narrative had a lot to do with it.
Fenstermaker talks about big ideas. The game did indeed have big ideas. It is about time that we had a game challenge the cliche dogma of fantasy religions and certitude. But the execution is not there. To his credit, he understands why we could care less about Abydon, Ondra, Woedica, Eothas, etc. That's not us being indifferent, that's them being absent for virtually 3/4th of the game outside of "lore." I didn't give a shit about Helm, Mystra, etc. in Baldur's Gate, either, despite the "lore," so it's not a benefit of familiarity. It's a problem with the narrative having little to do with the gods until Thaos lays it all out for you, and at this stage you've not known the gods for long enough for them to matter. I'll hope for improvement, to this end, because he understands the problem. Still, judging by what I saw out of the Ondra interaction in White March 2, they still don't quite get it.
This leads me to the bigger problem: he does not understand, and continues to ignore, that the characters in Pillars of Eternity were, by and large, boring, and thus depending on the characters to make the player emotionally invested/involved is not going to work. Why should I care about people such as Aloth, Sagani, Hiravias, etc., who just randomly hook up with the main character and barely says/does anything of value early on? Characters are not compelling just because they have their own personalities, motivations, and help to develop a theme. Characters are compelling because they make us sympathize with them, or like them, or hate them, or get a kick out of talking to them. Very few characters in Pillars of Eternity are able to do any of this, and that's a basic weakness that the writers need to address before talking up the big ideas for the second game.
As for Fenstermaker's description of how they came up with the story for Pillars of Eternity, I don't think it's as much of a problem as it is that they ended up with a story that no one felt too excited about. That should be a warning to you, right then and there, that the player might not respond very well to the story - when your own design team had issues warming up to it. Next time, don't just settle for "okay," especially in a project for your long time fans.
Finally, it sucks that we still don't know anything about what exactly they cut from Chris's design, outside of it not being necessary, but by this time we've come to accept that Avellone and the rest of Obsidian just wants to move on. Fine by me, but I'll forever wonder whether the man who gave us Planescape: Torment could've saved this project from emotional irrelevance.