Well, I agree that FF and SH games are too different to be compared directly. Don't know about the whole story of FF as I have stopped playing it, but having finished SH3 twice, I think the story of SH3 is pretty interesting.
And BTW, SH3 also had my heart pounding at the later stages. The visual effect is simply great and disturbing. Discounting AA and higher resolution, the in game screen looks really close to the previous released shots.