The 'Big Bad' was certainly nebulous and uncertain. I think we can all agree with that. Moreover, I find the cloudiness quite appropriate. S6 was not about gods or monsters--it was about inactions and the subsequent consequences of those inactions. I've seen innumerable complaints about S6, but I, however, welcomed the dark tone the series took. It was absolutely necessary to pull the characters apart. For five years Buffy, Willow, and Xander stood, more or less, side by side; they fought together, cried together, and most importantly, stayed together. A departure from their unity is exactly what needed to happen. Suddenly every character is alone and fending for themselves--Giles, the quintessential voice of reason, leaves; Dawn is often ignored; Tara deserts Willow (and I can also argure that Willow deserts herself); Xander and Anya break away from each other long before their wedding day; Buffy becomes a supreme isolationist; and Spike, well, has been alone for quite sometime, only in S6 he grapples with his newfound epiphany. Life is somehow more disrupted, more dangerous than it has ever been before--and this is without the menace of a super-powerful 'Big Bad'. I feel that this depravity was absolutely necessary to the narrative for it strangely gives the show back its life force.
I understand the many views fans have of S6 and, after all, we are all entitled to our opinions. However, I do not know how the series could have worked appropriately if there wasn't this separation between the Scoobies. As far back (and possibly further) as 'Restless' we are introduced to the fears that our core characters inherently possess. Interestingly enough, 'Restless' was a season finale, which is why I believe it holds great significance in the whole of the series. S6 seems to be reminiscent of all these deep and lurking subconscious psychoses and contemplations--Willow's retreat to the dark side, Xander's abandonment of Anya, Giles' departure, Buffy's anemic response to being the Slayer--these issues were (mostly) overlooked in the fifth season. This seems to be quite a deliberate process on Joss' part. In the scope of a series that as been unfolding for six years, it seems only prudent to invoke a disunity between the Scoobies. 'Restless' was a product of their unity--a consequence for a collaboration (the spell in 'Primeval') that was somehow wrong. Now in the sixth season those fears are addressed with searing backlashes for all--hence, the depravity, the loneliness, the lies.
But I digress. The question at hand remains: Who was the real 'Big Bad'? I say that it is not the Scoobies, but their fears. You could argue with me that their fears are apart of them and therefore the Scoobies are still the 'Big Bad', but I'll retort right back. The profundity of their fears is uncontrollable; they cannot adequately recognize or suppress them. This day has been coming for two years as 'Restless' proves. The Troika were what is called a Hitchcockian MacGuffin--a threat that is at once real, but in the end, is merely a backdrop for a larger threat looming in the horizon.
In closing, the nature to destroy ourselves is a part of human nature. Ultimately, this destruction is regretably inevitable and there is little we can do to stop it. 'Buffy the Vampire Slayer' is rather evocative because it does not shy away from the dark side of the human condition. We've seen it with Faith; we've seen it with Buffy; and now we've seen it with Willow, as well.
[If anyone is still reading, thank you. I like to write about film and television. I find it utterly fascinating to disect narratives and genre. That's why these forums are fabulous.]