Technically, it's severely broken... even if you don't happen to have a version that's riddled with bugs (beneficial or not, a bug is a bug), the Vanish-Doom/X-Zone trick is far, far too powerful, and totally breaks the game... far more so than any problems in FF7-10. ("So don't use it" is not an excuse. That's like telling people not to use infinite combos in a fighting game. They shouldn't be there in the first place, and proper testing would've gotten rid of them.)
From a writing standpoint, it's genuinely awful. You have fourteen playable characters, not a one of which is actually crucial to the main storyline. Every single one of them could have been excised from the game completely with minimal changes in the writing. To be more specific:
* Edgar & Sabin: The only tie these two have is to each other.
* Locke & Celes: Same story. No relation to anything except each other. Celes' magic-infusion plot thread is completely forgotten shortly after it is mentioned.
* Cyan & Gau: Nothing to do with anyone but themselves. Any character whose primary development comes in the form of an optional sidequest is pretty ancillary by definition.
* Mog, Umaro, Gogo: These three barely have anything to do, period.
* Setzer: A painfully transparent excuse to introduce the airships. Even his World of Ruin sidequest is airship-related.
* Relm, Shadow and Strago: These three comprise an unrelated subplot that can only get resolved if you happen to meet a few specific criteria, and get lucky (with the dreams).
* Terra: The only one with a real tie to the main plot, but even her connection is tenuous enough for her to receive no real resolution to her conflicts, and play no role in the climax and resolution of the story. She could just as well have been just another random party member.
I've had the argument presented to me that this lack of involvement is the point of the whole endeavor, to present that the theme of the story is regular people standing up for a cause, so the individuals don't really need a direct cause-and-effect link to the primary goings-on. That may be, but it doesn't excuse the slipshod writing and lack of any actual character resolution. A story is about more than just themes. It's about characters. This "day-in-the-life" approach is ineffectual when dealing with events that large in scope.
The actual main character of the game, Kefka, completely disappears at the midway point, and is reduced from being a genuinely engaging villain to a spectre and what is essentially a cameo at the very end. Any direction the plot had up through the first half of the game falls to pieces with the World of Ruin. Without the actual villain to provide an impetus to continue, there's no point. He was the most compelling member of the cast, and after he achieved his goal, he turned into a very generic "destroy the world" baddie with no real dialogue to speak of. After he exits stage left, the focus then falls to the individual characters to support the progress of the story, and they are just too sketchily characterized to be up to the task.
This is just bad writing by any meaningful standard, and "it's only a videogame" doesn't excuse that. An RPG survives on its story, and there simply isn't much of one to FF6. Its castmembers have virtually no ties to one another, beyond what and when the game's flow decides is convenient. Outside of the above-mentioned cliques, few of them ever interact with one another, either. Edgar talks to Celes once, as I recall, and there's a handful of character-developing scenes in the early hours, but these soon give way to... well, not much, to be honest. Personally, I would have been far more impressed if the game had followed through on its end-of-the-world scenario, and actually made Celes' would-be suicide the final scene in the game. Had that been the case, I would take back every negative thing said here, simply for the utter courage such a decision would take. But of course, that can't happen with such a high-profile series.
I don't say all of this in hindsight. I didn't care for how it all played out back in the day, either, when the game was new on the SNES. The game looked and sounded great, but there wasn't enough GAME there for it to be worth all the trouble.