From a storytelling perspective, although it would be difficult to pull off, I have often considered having the BBEG be not nearly as obvious. Think of Loki/Loge, Mephsitopholes, the Master, Xellos, and the like. Really charming blokes, who are incredibly skillful liars, excellent company, and more than willing to take the facade of the disinterest third party. They are concealing the poisoned dagger of their words and actions, until they are at the disadvantage.
Or the "BBEG" who isn't evil at all, just on the opposite side of the PCs. Cardinal Richelieu falls into that category. Q might, although he has done some nasty things (setting in motion an event that would prevent the existence of humanity is a particularly evil deed for someone who just wants to have a little fun torturing his favorite plaything).
The PCs might run into no end of trouble when they realize they've been on the wrong side the entire time. If they're Murderhobos like many PC groups, they might not care.