I liked in FF7 Cloud was the generic soldier, is captured by Shinra and experimented on. However, then it turns out that he was a failure, wasn't given a tattoo, and then turns out to be stronger than Sephiroth...or was that Hojo's intention all along? I have no idea, because Hojo was team Sephiroth until the end and didn't seem to care when Cloud proves himself and kills him.
FF8 will probably win, but I unironically like the game knowing how bad it is. My vote is for FF4. All the deaths that turn out not to be deaths completely devalued all their earlier sacrifices that weren't really sacrifices.