Skarner is my most played champ in the jungle, his ultimate is flat out amazing in lower Elo, the reason why is because any champion with a giant KILL THIS FUCKER indication does well in that general bracket.
But as you go against skilled APC and ADC, they generally are much more smarter to recognize the need to get a QSS or Zhonya ASAP when they have damage items, thus negating a lot of his potential team play.
I love him nonetheless, but there's a reason he's not popular imo. That could change if more and more people realize you can close the gap super fast with W and Righteous Glory.
Not only that, I don't think a lot of people have quite fully gotten over the changes that were made to him like a year (?) ago. He lost a lot of his damage and stickiness which is what people loved him for. He's definitely still incredibly strong, but he has his clear strength and weakness.
To quote Phreak: Pro's only like using the most bull shit champions they can get their hands on. Skarner doesn't really fall under that category.