I've read the entirety of the THR, and I was left feeling very similarly about Phase 2. I don't want to get into spoiler territory with my opinions, but I will say that Phase 3 went back to what I loved about Phase 1 and really stuck the landing for the most part. Phase 2 feels like an anomaly to me, and I bet it will to the article author when they finish THR as well.
During one of our discussions of Phase 2, one of my librarian friends explained the term "new adult fiction" to me and suddenly everything made sense. While it might not fit exactly, the article's mention of the Phase 2 books feeling like YA books makes the term feel at least a little pertinent. I think the authors in this phase were going for that sort of style.
I really don't want to hate on Phase 2 because I think THR was an awesome initiative overall, but... something about it just didn't click for me.