I like the way Pop thinks. However, I disagree that the long term villain is best layered and complex. I say this to modify why he's saying, not completely argue against it. I think the long term antagonist structure (I use the phrase "antagonist structure" to refer to a system that allows for multiple villains and complex relationships between them) is best layered and complex. Aside from characters like Irenicus where you peel away to uncover the whole plan, there's also the possibility of organizations, formal and informal, that you peel away to find out the whole plan of the organization as well as the head of it. It's a relatively common mechanic. The main difference with what Pop is saying is that it leaves room for a mustache twirler at the top of the antagonistic structure.
I want to think of a good example of this but the main thing going through my head is Xenogears. While Xenogears had a very complex antagonist structure with Grafh, Miang, Deus, Shevat, Cain, the Gazelle ministry and the lot. Deus is ultimately the prime villain, however without the relationships with all the others it could have been quite dull. I wish I could think of a more popularly known example of a complex structure of villains that worked.
However, I think as an example, Deus works incredibly well as "meaningful evil."