There are quite many AF-D lenses if not all that outperform you AI-S lenses. Actually almost all AF-D version is better in terms of IQ.
Only if you think about zooms, in which case you're correct. In fact the only AF-D lens I own is a zoom: The 35-80/4-5.6 AFD. I
love that lens and I wished Canon had something similar in FD version. This is almost everything I want in a zoom lens: covers most used focal lengths, sharp, contrasty, little distortion, and weights like a prime.
In primes the story is a bit different. When the AF line was created, many of the first prime lenses that were picked, used the optical design of the (inferior) Series E lenses, not the (superior) AI primes. Two examples:
The 28/2.8. In AIS form this is one of the best Nikkors ever. For the AF version, NIkon used the cheapened-down 5 elements formula of the
Series E 28/2.8. The AFD is the same design.
The 35/2.0. In AI and pre-AI form this is an universally lauded Nikkor lens that traces its origins back to the Nikkor-O of 1965. I owned those two versions btw.
The AFD 35/2 is a new, simplified version that has none of the marvellous qualities of the predecessor.
There are more examples of course, what about the 70-210/4 AF and AFD? Another Series E lens. Nikon, instead of giving you the awesome 80-200 of the AI world., gives you the cheapened down stuff. But, well, much better zoom lenses came later.
Then there were better prime lenses in the form of AF-G lenses, but those are unusable on manual focus cameras. Thus, for me, those are a waste of money.