Size, Weight, Cost. The Micro-Nikkor 200/4 AF-D is one of the sharpest lenses that Nikon ever made. It is big.
The manual focus Micro-Nikkor, a bit smaller and lighter- not as sharp. Sharper than the 200/4 Ais.
The 200/4 Ais is small, light, and not expensive. Plenty sharp on my Df.
Shooting a D800 and above, the Micro-Nikkor is sharper. I also had the older manual focus Micro-Nikkor 200/4, very sharp. BUT- the AF lens is better.