Very good advice from
@Ragpuppy87 there. The more you are exposed to a villain before you realize that they are the force you need to fight against, the more compelling the fight becomes. Sometimes they're shown in a villainous light the whole way; sometimes they appear like a decent person until the reveal. Either way can be effective.
One thing that hasn't been discussed yet (unless I missed it) is that the best Puppetmaster-type villains are the ones that
manipulate peoples' motivations (especially the motivations of other not-totally-villainous antagonists) - by tricking them (with lies or with schemes), threatening them, swaying legitimate institutions the antagonist belongs to, finding a way to offer what that antagonist desires, or some combination of those. A puppetmaster isn't merely someone who hides in the shadows while they send their minions at you! A puppetmaster is a villain that pulls strings to (mostly non-violently) force people to do their bidding.
Azula from
Avatar: The Last Airbender is a fantastic example of a Puppetmaster villain (while also being an action girl). For a much more brutal version of puppetmasters,
Psychopass is absolutely full of them, with a miles-long tableau of puppetmasters controlling other puppetmasters.