The greatest champions globally to counter Aphelios include Naafiri, Skarner, and Gragas. These champs are all great at countering Aphelios with win rates over 60%. Even if these Aphelios counter picks are not played in the same position as you, it's not a good idea to play him into any of these matchups. They will usually destroy Aphelios.
Conversely, if the opposite team choses either Rumble or Kennen, Aphelios mains should seriously consider picking him, as he easily crushes these selections with win rates over 53% against each ofthem.