Using this method of campaign construction makes that temptation all the harder to avoid. More so than any other non-player character, a villain must be tailored to the setting in which he appears. A quick examination of science fiction literature, TV shows, and movies make that pretty clear. The best villains are those that carry with them something of their settings' ethos and spirit - even if only in a negative way. Indeed, it's probably best for the long-term health of the campaign if its primary villain not appear in every single scenario or storyline.
Nothing spoils even the best villains like overuse.
That's why you should also give some thought to the other, lesser villains that might appear in your game. These villains may or may not be connected to the primary villain we've been discussing. Again, it's always important to think about the role and purpose of villains in your campaign. Since they don't necessarily fulfill a campaign-wide function, their place in the setting isn't as immediately obvious. All of these are valid reasons to use secondary villains.