Steve Jobs died just over a year after antennagate. He had already been extremely sick for years at that point.
I'm not sure what point you're trying to make, but he was still CEO at that point (his biography has a section about how he dealt with the antennagate issue) after having made a recovery from the transplant.
I think we won't see how Apples management really works until there's a new product space that Apple entirely misses, and I don't think we've seen that yet (it could be AI, VR, or something entirely different we haven't thought of). If they miss that just like Microsoft did in the tablet / mobile space, then we can start comparing Tim Cook to Ballmer.