Is VI overrated? IMO...yes.
It does get more credit than it deserves and the game does have some lackluster elements. Despite this, it doesn't change my opinion that in comparison to the main series, it is both my favorite and the one I feel is actually the best in the series cause it does fulfill my expectations for a RPG.
I love its world design and art direction, not only showing the best of Amano but making a good steam-punk world which I completely adore. Its artistic vision of portraying the entire game as a giant opera with an operatic musical score, a truly evil villain, comic relief, earth shattering events and even a curtain call. I truly feel VI is the first game in the series to have a well thought out and well executed artistic vision.
It still has my favorite cast of characters and over the years I've learned to appreciate and love every one of them which is something I can't say for the rest of the series with the exception of IV and XII.
VI's cast is one of the few that shows you can have a strong cast and not have to have everyone have some personal trauma to overcome. Yes a lot of characters have sad events in their pasts but only Locke, Cyan, and Shadow allow themselves to be controlled by it. Other characters are actually bothered by the here and now which is most apparent in Celes and Terra. Granted not everyone in the cast is deep. Mog, Umaro, and Gogo are more like "extra hidden characters" than thought provoking thespians. Yet I feel its ok and hardly detracts from the game and story.
The plot, takes the old cliche of "rebels vs. evil empire" but I feel it brought new elements to it all. It was the first to show a more gray area in all this, with Celes and General Leo who serve the empire but are actually noble and good people. Yet I feel most people focus too much on this concept, I feel the story really shines in its theme of "magic" and history repeating itself. How many fantasy games feature a story where the cornerstone of fantasy elements is actually dangerous and considered evil? Some have forbidden magic and power; II, IV, V, and VII have stories that focus on a forbidden power within the normal accepted doctrine of magic and psychic ability but VI is blatantly says its magic in general is unnatural and the concept is quite striking.
Combine this with the WoR plot twist and I feel the story speaks on greater volumes than its brethren in the series. Speaking of the WoR, I love it, I enjoy the fact that the game allows the player to explore the world they once knew and see the cataclysmic consequences of the parties failure to stop Kefka and Ghestahl. The freedom to explore is also much appreciated, I enjoy story but I dislike linear gameplay and hand holding. One thing about RPGs I like is that they are somewhat open ended and the old school games promote exploration. This concept has slowly been removed from the series and as the genre has changed, I appreciate this element more an more. The WoR was a breath of fresh air considering the first half is terribly linear. The player is left to make their own decision about the event unlike other games where the story dictates how you should feel and what you should do.
X was a game that told you how to feel about the world but overall I found Spira to be relatively peaceful and most of the time down right boring. The mass destruction Sin caused nothing more than ruins from ancient civilizations, it always felt like we missed the big cataclysm and we're just watching the aftermath after everything has calmed down. We only witness Sin destroy one small village and even then I found it difficult to be sad cause Sin's involvement was more indirect than pure maliciousness.
In VI, you saw these places in their prime and watched as they tried desperately to survive after the world was devastated. The story doesn't tell the player "this is sad or terrible" its obvious and the impact is felt better than it was in other games that try to utilize world shattering events. I feel its better shown cause it allowed the player to use their own intellect to determine the devastation instead of stating the obvious and showing little to back it up.
Another point I would like to bring up is that I felt VI was the game that perfected using music to enhance story with emotion. All previous FFs have this but I felt that almost every track in VI heightens the emotions and the players feeling. It not only had a damn good soundtrack but used it beautifully to bring to life many of the most powerful moments of the game. Many of the previous games did this of course but I feel VI did it with most of the soundtrack, its opera inspired soundtrack played beautifully with the games artistic and emotional themes.
If the game has a serious drawback, its in gameplay. I mentioned most of my complaints in detail in the sister thread on VII. To put it simply, mediocre difficulty, overpowered skills like Tools and Blitz, overpowered magic (though it fits with the story) and a customization system that can make every character an omnipotent deity. Even then, I have fun with the gameplay and I feel every other element of the game makes up for it. Hell, its not even the worst system IMO cause I at least still have fun with it even if it is non-challenging.