This is actually really tough. I think FFT has a great initial setup of a dark political story, but as the game progresses it tends to shift more to a standard save the world from the demons plot. The fact that the story characters basically drop from the plot completely once they join your party doesn't help matters either.

FFIX on the other hand has a plot that's more standard fantasy fare right from the get go but it really handles it quite masterfully, particularly in the introductory sections. The plot also tends to veer into being an homage to past game plots, but that doesn't bother me too much especially with the unique spin and charm characters like Vivi and the other black mages bring to the game. Much like FFT this story tends to devolve in the later sections, where at points it seems like nothing more is going on than an eidolon pissing contest. Still, I feel like from Terra on the story sticks the landing pretty well. I'm not sure I feel the same way about FFT, although the epilogue is on point.

Honestly, I'm not 100% sure, but I think when it comes down to it my decision is made by Vivi and his arc. I'm sure some people who like to pretend character and story are nice distinct categories would complain I'm deciding based on "character" rather than "story.". Those people are wrong, because character is not a distinct category from story. Characters make up a story and the journey a character takes is a pivotal part of the story. I'm going with FFIX.