@Seth: bringing together of the Virgin airlines in FF program really happened recently: one would have thought given that they shared the same name, this was a feature from the get-go.
That being said, FF earning/redemption is only really one small component nowadays. I don't agree with Ben's "smaller growth of alliances," and looking at statistical numbers of membership growth, that already proves that wrong. Rather, it's now not specifically looking at alliances, but relying on deep partnerships because codesharing and shared frequent flyer benefits are pretty basic now in the aviation industry. And it makes sense given the size of the alliances: back then, airlines that belonged in an alliance had the upper-edge but as more airlines have those benefits, there needs to be other ways to distinguish the airline.