I'll take a shot in the dark here since I can't speak for the jQuery team of why I wouldn't use JSDoc. JSDoc, at least the last time I checked, didn't have any clean way to support method overloading (or parameter shifting...whatever name you want to give it here) and jQuery uses this all over the place. Let's take a simple common example with .animate():
.animate({ height: 5 })
.animate({ height: 5 }, 100)
.animate({ height: 5 }, 100, "linear")
.animate({ height: 5 }, 100, "linear", func)
.animate({ height: 5 }, 100, func)
.animate({ height: 5 }, func)
.animate({ height: 5 }, { duration: 100, queue: false })
.animate({ height: 5 }, { duration: 100, easing: "linear" })
.animate({ height: 5 }, { duration: 100, easing: "linear", complete: func })
All of these are valid, since parameter types are checked and shifted as needed to support as any overload scenarios as possible...this just confuses the hell out of JSDoc, there's no clean way to add these optional parameters to the documentation. Please correct me if this has changed, but last I looked (and probably the last time the team took a look) this was still the case.
Another potential consideration is how some methods are generated when jQuery runs, for example (one of many), almost all the event handler shortcuts are generated in a loop similar behavior for other methods...how would you document these? JSDoc generation just really doesn't work well here.
