The top champs out of lane to counter Skarner include Kog'Maw, Varus, and Lucian. These champions are all good at countering Skarner with win rates over 61%. Even if these Skarner counter picks are not used in the same position as you, it's not smart to take him into one of these matchups. They will likely crush Skarner.
Yet, if the opposite team brings either Volibear or Talon, Skarner mains should seriously think about selecting him, as he easily destroys these selections with win rates over 56% against each ofthem.