Realignment: Neutral Evil

     Neutral Evil, like Neutral Good, is probably used mostly as a stock default alignment for villains. For those generic bad guys who you don't need to bother putting a lot of characterization and backstory into, NE allows you to give them a basic, workable (if two-dimensional) character type without a lot of preparation.
     But, as an alternative, I think NE also makes a great alignment for a major villain or mastermind. The same aspects of Neutrality that make common enemies simple can also make a major villain work well.
     See, neutrality on the law-chaos axis allows you to focus more on the good-evil axis. In this case, it give you free reign to develop your villain's evil side, without having to worry about any kind of constraints. A NE villain can be completely focused on whatever it is that makes them focused, which means sometimes they may work with the law, and other times they will break it. 

     What immediately jumps to mind is a politician or corporate-type villain. These are people who will use the law when it suits them, but are perfectly willing to work back-alley deals when necessary. They may be legit on the outside, and many of their operations will be perfectly above-board (even if ruthless and amoral), but they will also work the shadows when they need to close the deal. The more interesting aspects of these types of villains, of course, is that they may not even think of themselves as evil. Their motivations are purely selfish (usually greedy for money and/or power), and they don't care who they hurt on their way to the top, which definitely makes them evil. But they probably still consider themselves legitimate businessmen and/or politicians as opposed to mobsters. Hell, organized crime members are probably more Lawful Evil than a politician or corporate bigwig. At least the mafia have some sense of loyalty (or at least a healthy enough fear of what happens to mobsters who go around betraying other mobsters).
     A lot of it boils down to what you want out of your villain. This is an interesting, and difficult decision to make. A good villain has good motivations. The forces that drive a villain are what make them memorable, as opposed to the faceless hordes of common baddies that your PCs will wade through. A major villain should have an obsessive goal, something that they want so badly that they are willing to shake loose of any sense of morality that most people would submit to.
     Neutral Evil is a great alignment for this, because it keeps them focused on the evil and allows them leeway on how to interact with law and chaos. An unconstrained villain, conversely, is able to be much more focused and single-minded.
     So, remember, great villains need to have an ultimate goal, and they need to be free to pursue that goal in whatever means necessary. Even if they occasionally don't commit crimes.