This era in JRPG was all about subverting the tropes, both in story and gameplay, and this was especially true with Squaresoft .

FF8 is probably my favourite example of that. You can take the story at face value as the old Good vs Evil archetype, but if you dig a little and read between the lines you realize that it doesn't hold and everything is in a grey area:
>Recruit orphans in order to turn them into soldiers, knowingly make them use a weapon which damages their brain. The Good guys.
>Ultimecia knows SeeD are coming to kill her and that it's inevitable because it already happened so controlling time & space is her only way to survive. Her only motive is survival.

That's the grand lines but there is more of that in the details, like how they end up making peace with Galbadia, Seifer being full of grey areas too.
At the end of Disc 1 Squall thinks to himself "there is no bad guy, only two parties with different points of views" and it doesn't just apply to the situation at the end of disc 1 but to the entire game.
Also when the mayor Horizon says they could solve the conflict if they just stopped and talked, which Squall's brushes off as naive because of his military upbringing, or should I say indoctrination, this too could apply to the entire game. If Squall and Ultimecia had a chat they'd realize they only want to kill each others BECAUSE the one wants to kill the other and vice versa. Though of course this is not possible because of the theme of fate which is so proeminent in the entire game, but that's an entire other topic entirely.