I liked it. It's so true. I remember that while playing Xenosaga I what bugged me a lot was how vague some things were. I couldn't understand why everybody was after the Zohar, it was left unexplained, or why the emulators were created, etc. And the way our party just left MOMO, even though they already knew the enemy was searching for her, that was a clear plot mistake. I didn't notice anything else, though. But the article author noticed a lot!
I think the "too vague" flaw is in all three games, really, it was never fixed. We only get to know something at the very end, instead of bit by bit like we should've. Instead of creating an air of mystery, such storytelling just makes everything feel pointless, as there are no answers to too many questions per game. I think each game should've provided enough answers in and of itself to feel satisfying.
As for the ending of the whole trilogy, even though it provides answers, it feels disconnected from all three games, like deux ex machina. Simply because we couldn't guess any of it. Yeah, there was foreshadowing, but it wasn't enough. The fact that KOS-MOS' eyes sometimes went blue or chaos could kill a Gnosis by touch or Shion could see Nephilim, etc... that just wasn't enough. I still think those three to be full-blown Deus Ex Machinas. It's almost like the writer didn't know how to connect "the truth" to the rest of the story, so instead of having us gradually discover it for ourselves, he just dumped the whole info on us at the very end.
I hope I don't sound too negative. I still love the games, regardless of all that. But it's certainly true that the storytelling could be done a lot better.