As much as I admire John Carmack's work id doesn't rely solely on him. They have some of the greatest artists out there; and a couple other gifted coders from what I hear.
For sure if/when he goes things will be different, but the company isn't gonna implode or stop making great games. They'll just hire a new coder or two and go on.
But the main thing is that with the large advances of hardware renderers are gonna evolve at a much slower pace. Within a couple years new games engines will be more in the form of updates of previous engines, not full blown new ones. Much like with the pre-rendered engines. And Carmack has said that himself a couple times in the last two years. So, 'engine coders' will become less and less required and coders are gonna get specialized in various areas.
Doom3 and the upcoming Unreal3 engines are huge leaps from the previous generations, but it's unlikely we'll witness such thing again. The whole lie of "photorealistic quality" is getting truer and truer every year. Just look at the Gears of Wars screenshots, they're better than some pre-rendered work of just 5 years ago..
That said, I can't wait to see what the id guys are working on.