Zilean's ult has an inbuilt weakness. Several, actually.
If he's ulting a teammate, he's not able to resurrect himself (duh.) Zilean is super fucking squishy, and his ult is fairly obvious and doesn't last very long. If Zilean doesn't ult himself, he can be bursted down to prevent him from aiding his team.
If Zilean DOES ult himself, he runs into the problem of not being a hard carry: Zilean can't solo an enemy team unless he's MASSIVELY fed and is building full AP. So, if he's ulting himself he needs to make use of that (by being a meatshield and the like.)
His ult is easy to counter: If you know the enemy team has Zilean, watch for the ult animation. Target everyone but the person with the ult (ideally you drop them very low, then leave them alone till the ult runs out, then murder them.) Additionally, since Zilean is so squishy it is feasible to target him first, thus either forcing him to burn his ult on himself or die.
His ult is one of the best designed abilities in League, it promotes a lot of strategy and tactical play. I would be GREATLY disappointed if they removed it, as the 'Can't Killean the Zilean' video on youtube would no longer give me tears of laughter, but of sadness. Highly recommend watching that video, BTW.