...I'll be brief because obviously I'm in the minority on liking Xenosaga III. Yes, XS3 has some stupid plot points. However, they don't interact with the rest of the game's plot TOO much, so I can't really be on board for too much XS3 Disc 2 hate. I mean, take Final Fantasy VII plot. It is now revealed at the end that Tifa was really Mary Magdalene's clone! .... this is impossibly dumb, but it ultimately doesn't make much difference and affects the rest of the story not at all. About 90% of XS3's plot stil works if we replace chaos as "generic mysterious guardian of good" and KOS-MOS as just a really advanced robot.
On the offensive deal, well, this is ultimately personal for everyone. Still, this is ultimately where inanity saves the day a bit. Saying "Jesus was an evil demon, and it was all a plot to send everyone to hell and gain ultimate power, and Judas totally saved the day" is fairly offensive to me. (This is the backstory to Final Fantasy Tactics, though they did change the names, so they can take refuge in that at least. Also, it's undoubtedly interesting as well as offensive, at least.) Saying "Jesus was secretly a space cowboy on a quest to find the best burrito ever with his Vensuian Chimp, Christmas, from whom the holiday is named after" is just roll-your-eyes-and-move-on, to me at least. I'll grant that XS3 took the space burrito plot sadly seriously, which is a mark against it, but ultimately I myself can't work up too much offense. I did read "The Da Vinci Code" after all, and moderately enjoyed it as fiction (though that book ALSO needs to be thrown against the wall in several places), even despite Dan Brown rambling about "faction" and talking about how its plot should totally be taken seriously.
As for Grandia III, that strikes me as a whole different level of fail. It just breaks so many *obvious* guidelines of how to write a decent plot - hell, even a generic yet decent tropetastic plot. The XS3 writer needs a talk, yes, but the G3 writer needs to be expelled as a hopeless case. Keeping the exact same movies and scenes, but rewriting the script to make a half an ounce of sense... I could have done far better in just two days. Seriously, WTF. And yeah, Emelious is at the center of a lot of this. Hoping for villains to reform is all well and good, and writing Alfina as having a character flaw of "always trusts her brother even when she blatantly shouldn't" would also have been fine. The actual writing ends up so idiotic that... ugh. I think I'll stop now, because there's just so many parts that even minor fixes would have made better.
Yeah, I suppose what I'm saying is XS3 Disc 2 plot > Grandia III post-Miranda/Alonso plot. At least the first has some redeeming factors.