The trouble with X-Men of course is that it's an ongoing series (since the 1960s) and so they have to keep trying to find new ways to approach the question.
The problem here is that Joss has to work within his own formula. So far, he has always been creating seasonal Big Bads and I doubt that he'll break the tradition. But he can't turn into BB neither Buffy nor humanity. (Although I think Buffy as real BB would be the ultimate cool.) It's just not a viable option. His audience won't accept it.
So I think he'll dodge the problem he created, simplify the situation and make The New Initiative the BB.
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The problem here is that Joss has to work within his own formula. So far, he has always been creating seasonal Big Bads and I doubt that he'll break the tradition. But he can't turn into BB neither Buffy nor humanity. (Although I think Buffy as real BB would be the ultimate cool.) It's just not a viable option. His audience won't accept it.
So I think he'll dodge the problem he created, simplify the situation and make The New Initiative the BB.