The Bond franchise is the most obvious example of the flailing failure to find a replacement. The Chinese-industrial axis in Tomorrow Never Dies didn't quite resonate, and Le Chiffre worked brilliantly as a nemesis in the Casino Royale remake, but the organization that theoretically employed him was a massive dud in Quantum of Solace. The franchise is on hold right now, at least in major part because of MGM's major financial difficulties, but if a studio was going to cut an expensive, long-running process, Bond's an anti-hero without a mission these days, and worth shelving until he can find a new rationale.
Contemporary spy shows like 24 or Spooks have survived in part by addressing an array of villains. But terrorism of the Osama bin Laden variety's a bit...diffuse, and it's hard to have a clash of equals when the visions of the adversaries are a question of modernity and its destruction, not different visions of progress. It's not a duel, it's much messier, and in the end, al Qaeda's going to lose, which takes a lot of the suspense out of things. Strictly for the purposes of storytelling, it's nice to have the Russians back.