““We were finally at a state in the project where we could play through the whole [game]. And it became very clear that we were missing the large final location that was going to tie the story together and have a satisfying action-filled payoff,” Shen said. “I was both implementing the main quest and leading the quest design team, so I had absolutely no time. The entire quest design team was already overbooked.””
The quest design team being overbooked and not having time certainly explains a lot.
I would have been fine with a new game+ story but the main story got completely revamped for the second playthrough. Not just a few unique dialogue options.