Zilean hasn't been frequently played for a while now. The issue with Zilean is landing your ult and bombs. Most people think its easily done, but to do it effectively in solo queue without wasting it is very difficult, more your ult than bombs. You practically have to cast right before their death. As well most people don't even realise that they've been ulted by Zilean and run away when they should be going harder (this is mainly for bronze-silver and gold). In terms of utility, he's is up there. He has a slow, speed up, a revive and buttloads of dmg that can generate a stun, but choosing which 1 to use effectively is also not an easy task. Most people would rather just be lazy and pick blitzcrank, leona or morgaygay; very straightforward champions. Very few also pick Janna, Nami and Lulu as well. I believe the answer lies in how complicated these champs tend to be. They're squishy, their dmg isn't high like Annie's or Morgayay's, and to use these champs requires you to depend on your team being able to effectively use your utility as well as you being able to effectively provide the use of your utility.