There is no doubt that currently Tim Cook is the best person to run Apple in the short term. Apple also has the best executive team in the world and has several major products in the pipeline so the company will fine for the next few years. However in the long haul Apple is at serious risk of losing their way if Tim Cook remains as the CEO.
Steve Jobs has many exceptional talents including marketing and understanding of design, but his most important skill his incredible vision for products. Steve Jobs is so involved in the product development process that he has his name on patents for nearly all the major products that have come out of Apple in the past decade. He had the vision to know that the iPad, which was designed before the iPhone, was not ready for prime time and developed the iPhone first. This is an example of a situation where Tim Cook will not have the instincts to know what to do.
Tim Cook, for all of his talents, has shown little indication that he can serve Apple in the same product capacity. Apple is not an operations company and will be ill served without the right type of genius at the helm.
Vic Gondotra's story about a phone call from Steve Jobs further illustrates my point.
"So Vic, we have an urgent issue, one that I need addressed right away. I've already assigned someone from my team to help you, and I hope you can fix this tomorrow" said Steve.
"I've been looking at the Google logo on the iPhone and I'm not happy with the icon. The second O in Google doesn't have the right yellow gradient. It's just wrong and I'm going to have Greg fix it tomorrow. Is that okay with you?"
Tim Cook would never make that phone call.