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I know the FA and F4 bodies take advantage of the focal length information as relayed by AIS lenses, but beyond that, there's no difference in the functionality of the mount itself. The build quality is identical.
My understanding is that the actual lens designs were unchanged between AI and AIS lenses. A larger number of upgrades occured between non-AI and AI mounts, though many late non-AI lenses feature the same formulas as the later lenses.
There is a significant difference between these: AI has non-linear and AIS has linear aperture control. Meaning that you always should set the aperture directly on the lens instead of through the camera dial, when an AI lens is used. (this issue becomes critical if the AI lens is chip modified).
Focusing action tends to be stiffer on the AI generation, but the disadvantage is partly offset by the throw being longer than on the AIS type, so focusing acuracy especially for wide-angles was better. Many people hold the opinion that build quality and workmanship are better on the AI lenses, and I tend to agree.