I hated FFIV, so I'm not to sure about FFIVDS :/
Also I kinda wish they'd rewrite that scene from CT where
you revive Crono, because the entire thing was just handled sort of poorly. I don't have a problem with the Time Egg amounting to deus ex machina on a pretty blatant and massive scale. I AM annoyed that what WAS a fairly well done scene -- Crono getting killed -- was completely diminished by the fact that you replace him with a doll you won at the carnival.
What the fuck? Seriously.
Additionaly though there ARE some things in Trigger that sort of change the meaning of the story like
the entire Entity bit there. Not so much because of stupid ZOMG THE ENTITY IS THE PLAYER bollocks (And I can't think of any way anyone would even come to that conclusion unless they're incapable of parsing sentences. It's something they don't under) but because "Well, the Entity is near-death and wants us to see its memories" is NOT the same thing as "Well, the Entity wanted us to save it".