Karin Koenig says:
"Yuri,
I love you, but I know that our love can never be because of this obsession you have with Alice, so I'm going to do the next best thing, which is to travel back in time, hook up with your father who looks exactly like you, and give birth to you. How do you like those apples?"
That is the absolute craziest ending to a J-RPG I have ever seen. Pure genius. And it's not like the writers pulled it out of thin air at the last moment--there are clues that allude to the ending throughout the game, and they even made use of information you get about Yuri in Shadow Hearts 1.
Anyway, the highlight of the storyline for me was the sequences in Russia--that's where all of the plotting and characterization came together, and if the game had stopped at the end of the first disc I'd have been happy with the $25 I spent. The entire second disc was just icing on the cake for me--sweet, delicious icing.
The only tedious bit of the game for me was
the Man Festival, and that's only because I ran the one-on-one boss gauntlet to get to the 100th floor, only to have the Great Gama's Grand Slam connect with Joachim for a Game Over. I never did finish that.
Between the gameplay and the storytelling, I'm more excited about the new Shadow Hearts game than I am about FF12. Shadow Hearts has pretty much ruined me for just about all other J-RPGs.