I think that's one of the central dichotomies in comics today: is success making a good story or making money?
I think villains are just another aspect of the most popular heroes that it's hard to change. Sure, it's hard to make a new villain for Spider-Man or Superman or Batman, but it's also next to impossible to make a new friend or a new boss or new costume or new hairstyle work for them. Mainstream comics are always resistant to change. People just notice villains more.
Not that that article isn't dead on--I'm just saying that the resistance to change applies to villains, just like it applies to costumes or love interests. Both the reasons in that article and this resistance are reasons why new villains frequently fail.
Runaways was founded entirely on new villains--the Pride, the Gibborim, sort of Alex. The young X-men title whose name I can't remember introduced some new villains. I can't think of many smaller titles or the new villains they've introduced right now, but my point is that just as non-flagship titles can introduce new love interests or kill heroes, they also have greater success with villains.
I say villains should have to work their way up to the big time. Take some new guys from a less-popular title and start making them bigger threats in a logical way that treats past appearances and characterization with respect.
Another idea--make a new villain pop up in a few different titles and fight a few different heroes. See who they have chemistry with and which title the fans like them best in. Once you've picked the hero they go with, get a writer and artist who work well with the hero to write a story arc in which the new villain and the hero acquire a logical personal vendetta against each other.