In a series with rather generic stories, IV and VI got the best twists (considering the kind of stories RPGs had when they were released). My reasons for choosing VI as the best are several:
- It had an impressive cast (the lawful thief, the traitor, the brainwashed, the king, the disgraced knight, the carefree prince, the spellcaster past his prime, the selfish gambler, the mysterious warrior, etc), each with its own strengths and its own weaknesses. They wer all similar, but completely different. The first world gave you the characters and their introductions, the second gave you their reasons.
- The story develops itself naturally from the invasion to Narshe as a member of the empire to the final battle in the World of Balance. It grows as a snowball, adding characters as the events within the war reach them. Remember the Simpson's episode where Burns is "killed"? Remember how it all started with the school finding oil, and then develops naturally (Burns stealing it with the inclined tower, its first extraction destroying Bart's house, its toxins closing Moe's, etc, etc, etc) until the very climax where everyone has a reason to kill him? Well, VI is the same, its story grows and grows adding characters that hold a grudge against Kefka until the battle in the floating island and the destruction of the world.
- It gives you a second half where you are absolutely free to do everything. Contrary to the heavily scripted first part, the second is like a MMORPG. You choose where to go, with no rules, no order, only one objective: kill Kefka. You only need three characters (Celes, the one you start with in the world of Ruin, Sabin found in the first town you reach, and Setzer, whose airship is the only way to access the tower). If you want, you can find them all, and upon finding them, you learn more about their past: Setzer's love, Shadow's past, Terra's life, Cyan's family, etc. Those who say FFVI characters are weak or generic, it is because they didn't take the time to play the World of Ruin.
- The world is destroyed! How many games dare to do something like that? I remember Shadow sacrificing himself to save the party (didn't wait for him the first time I played :-(). The wasteland, everything brown (just like Gears of War ;-)). Remember typing ZELDA as your name in The Legend of Zelda? Remember the roguelikes? It is the same world, but completely different. The same cheerful characters are now depressed, without hope. Families are no longer complete, houses are no longer opened, paths are no longer opened, walls are no longer blocking. It is a different sense of oppression: the first one was about no freedom, the second is about no hope.
- Some people discuss whether Heath Ledger or Jack Nicholson is the best Joker. Imagine taking the best of both, and creating a single Joker. That is Kefka. He is extremely evil, but childish. He is completely mad, but knows perfectly how to reach his goals. He is cruel, and his laugh is memorable. But he is also dumb and will run away when outnumbered. I don't remember a game before it with such a final boss, one that would bounce around guards trying to run away in a moment and would order a castle to be destroyed and everyone inside to be killed in the next one.
The combat system was really generic, and the Magicite system didn't really help (in the end every character would know exactly the same spells as the others). There were also balance problems (there was little reason to use a spell other than Ultima to deal damage) and the World of Ruin was too free (the game came with a map with numbered towns that gave you an idea of the order in which you should travel), but without you were pretty much lost. You had to check every town for gossips, and in some cases enter dungeons or rather vague locations (I hated Locke and Gau). I understand why the World of Ruin gets more hate than the World of Balance, but that is part of the design: had it been scripted, I believe the player would have not been able to create such a strong link with the characters. Having to search and recruit them made you appreciate them more (and I have yet to find someone who didn't replay the game when he discovered Shadow could be saved!).
I am not saying the others (particularly VII) don't have these points. But I think the series reached a peak in storytelling and character development while at the same time having a really high technical quality (the over 20 minutes ending, for example). Final Fantasy VII made it mainstream, and for that I am thankful. But I think in order to reach it it needed to do some compromises (less amount of playable characters with a clear main one, more straightforward game, CGI, etc) that in the end made (ironically) FFVI even more unique.
Just my opinion.