Someone told me if you're mean ass hell to tifa and nice to aeris, tifa pushes aeris out of the way and dies instead, I tried it on the english version, that might be what you're talking about.
Anyway, my most shocking game play would have to be, Suikoden III, he doesn't get to control the castle. Gay little Thomas does.
I've been trying to find a copy of that game.
Part 2 had its share of surprises, though. I still don't understant why Joey turns evil, but can become good in the end still. To me it doesn't make sense.