It was a drastic departure from the rest of the series, even more than X because it actually had a different nature.
All the archetypes that had built up in the series starting with FFVII are there, or so it seems: bishi hero, brooding older sidekick, sexy ass-kicker who will probably be the love interest, a couple other buddies, all assembled somehow to take on the great evil plaguing the world and reveling in their evilness. Along the way, they discover that they are not so different from each other, decide their father knew what was best all along, maintain the confidence that they are still the good guys, the guy and girl realize they've been on screen together for longer than 30 minutes and need to start making babies as soon as the quest is over, etc.
Except...that isn't how it is.
You basic pretty blonde boy is Vaan, the hero of the story who...is not the hero of the story. He's a spectator, the main characters are three "sidekicks" you meat in the story: Ashe, the fugitive princess of the kingdom the story mostly takes place in, who is the true hero of the story; Basch, the old grizzled archetype with a chip on his shoulder; and Balthier, the Lando-Setzer lovechild that never was. All three have an exponentially greater stake in the conflict then your two "protagonists".
As for the whole evil thing, there's the tried-and-tested Evil Empire trying to...consolidate power, unite all the lands of Ivalice and create again a utopic nation the same fashion as had been done by, hm, Ashe's great-great....great grandfather.
I am seriously about to spoil this game hard, so don't read if you don't want to know.
Turns out this whole time there are a pantheon of ambivilent gods who control all human affairs, and were directly responsible for the creation of the old Golden Age, and now they have called for Ashe to destroy the empire using the most extreme means available (basically, do the same thing that the empire had been doing ((ie, nuking))). The Big Bad, Vayne son of the Emperor, who kills his father to become emperor, is also being led by a fallen god named Venat, and together are manipulating Ashe to destroy the Crystals created by the gods to give power to the mortals. They do this of course, by showing Ashe images of her dead husband, who appears as a ghost to tell her to go commit genocid (Vaan similarly is manipulated with the "ghost" of his brother).
So long story short, Ashe decides to fuck the gods, and destroys the Crystal so that teh EMPIRE can't use it anyway. This whole time, we see Vayne's perspective as well, where he decides to kill his father, the corrupt emporer, dissasemble the equally corrupt senate and become the new Overlord (Dynast-King in the story) to enact his utopia (he also has a kid brother who is very important to the story and adds plenty of depth to the whole empire scenario, but I don't want to get into that).
So the showdown is typically grand on top of Steam Tower (two bucks to whoever gets that reference) where Basch reconciles with his brother (another character that adds depth to the good? v evil? concept) and Vayne is mortally injured. After seeing his henchman prove weakened and useless, the Big Bad Venat does this http://www.youtube.com/watch?v=zgx4slhzNWs#t=2m45s
Uh wait, was that...the personification of evil, the stand-in for Lucifer, comforting and showing compassion for the puppet he had used to screw mankind? And wait...did he succeed
? And wait...what did he succeed at? He succeeded in...freeing mankind from the tyrannical and uncaring hands of their sociopathic gods. (He also gave up his immortality so that he could die along with his faithful servant.) The same gods whom the heroes had been questing for this whole time, who had bestowed magical gifts to them, they who were trying to destroy the "evil" empire with its "evil" ruler and ambitions.
To quote an observant user of TVTropes: "Ashe
is the Big Bad". ...Actually you probably should just read the TVTropes page.
Oh yeah, and that love story? Never happens. Vaan couldn't care less about Ashe's snatch, and Ashe is still obsessed with her dead husband.
That's just a barebones summarization of the serious deconstruction of the genre that goes on here through my simple analyisizing.
Now, alot of folks have criticized the changes, particularly the seeming unimportance of the decoy protagonist. As is the fact that, as I'm sure you discovered, the game seems to be more occupied with the immense exploration and questing than with the central story. But in fact that is one of the more genius moves in the development of this game. This whole big story, the complex backstory and political intrigue as seen through the eyes of a peasant kid from the streets doesn't mean a whole lot and probably doesn't make much sense. Instead, the aspiring treasure hunter is far more interested in exploring the world and having adventures (which is why Vaan is the avatar when not in cutscenes; talking with people, accepting quests, bartaring, learning things, developing). So being that the player avatar is
Vaan, and not Ashe, it is logical that the focus of the game sometimes is not on the plot, but in the playing.
Ah yes, playing, exploring, discovering...who the fuck put that in my RPG?
Anyway, I could go into how motherfucking beautiful the game looks, how I've never seen level designs like that before, how the writing and voiceacting is miles ahead of FFX, or the music is truly mesmorizing, but I believe I've written enough to bore everyone already.