Cook was viewed by some as a natural successor to Jobs. In his role as chief operating officer, he managed Apple's worldwide sales and operations, including management of its supply chain, services and support.

Perhaps more importantly, Cook has already had experience running Apple's day-to-day operations during Jobs' leaves of absence, including the period from January to the present. But there are questions about his ability to continue the spirit of innovation embodied by Jobs, whose headstrong management style inspired workers, and whose vision kept the company ahead of market trends.

"Steve Jobs has always been the visionary at Apple, and Tim Cook is the operations guy, and he's good. The problem may come in a couple of years when the company has to see things that can't be seen today," said Roger Kay, president of Endpoint Technologies Associates.

For sure, Jobs will remain at Apple as chairman, at least for now, and will be involved in design and product decisions as best he can. "Jobs will continue as chairman of [the] board, so you are talking about a guy who will continue to have influence on Apple's products ... for years to come," said Gartner analyst Michael Gartenberg.

But the state of Jobs' health is unclear, and in his letter to employees Wednesday he suggested his role will be lessened in the future. "I have always said if there ever came a day when I could no longer meet my duties and expectations as Apple's CEO, I would be the first to let you know. Unfortunately, that day has come," he wrote in the letter.