I don't think it makes the traditional heroes seem pointless. I think it keeps the conflicts varied. Not every story can be about a pure evil antagonist. That becomes formulaic.
And I don't think the anti-hero villains are quite as prevalent as you say. I see plenty of villains, like Purple Man, like Taskmaster, like Mr. Fear and most of the baddies in Daredevil, who are motivated by largely or purely selfish reasons. And I think some of your examples are a little exaggerated. I mean, take Secret Invasion for example. Yes, The Skrulls have motivations that kind of make sense. That doesn't make them anti-heroes. It just means they have a reason for doing what they do that follows some kind of logic, even it's still a bad idea, as opposed to "we will invade the Earth because."