FFVII compilation. I'm not sure why you would want to retcon the story like that.

I'm on the record for Xenogears and its facially shocking, but substance-devoid religion references, like the Ethos and child molestation and the scene where the Gears are crucified.

And now I'm going to argue...

Skyblade & Final Fantasy Tactics

Ramza didn't kill Delita because he was too busy trying to stop milennia-old demons from enslaving the world and killing everyone. Delita and Ramza both had the same objective - subverting the grand plotting of the nobility and clergy which had always led to the killing of innocents. Delita just did it through a lot of ambitious backstabbing. Plus they were friends and Ramza blames himself for Delita's sister's death. Delita's ending is perfect. He tries to stop the morally relativist cycle of ends justifying means by... employing a scheme of moral relativism of the ends justifying the means. He thought change was only possible through playing by the rules, and his ending is accordingly ironic. FFT is arguably the crown jewel of hardcore JRPGs and I think the player is thoroughly rewarded for its completion.

Wolf & Big Boss

Big Boss has been built up as a good guy since the original Metal Gear Solid retconned him and his status as Snake's father. Everyone in that game idolized him, and the Solid Snake in that game is a man wracked by grief and rage over killing his own father, leading to his complete disillusionment and distrust with the United States government and its special forces. Kojima sacrificed the original Metal Gear games in order to build a deeper story with relevant themes that go beyond a soldier on a mission. And Porable Ops and Peace Walker both dealt with the same subject matter because only Peace Walker was directed by Kojima. They were both games in which Big Boss dealt with The Boss' death because they had to be; we needed to see how Kojima intended to handle it. Lastly, at the end of MGS3, he only learned what The Boss had done, he still refused to understand why she had done it.

Have you listened to the bonus tapes towards the end of the game?