AIS is newer and has several additional features in addition to different optical engineering and coating formulations. One difference is that they provide additional data to the camera about what lens is mounted on it, some of which anticipated Matrix metering as is the case on the FA and some other later bodies. A common belief is that it changed the mechanics for Program mode, but AI lenses also work in program mode on the FA and others that have it, as long as you keep the aperture ring set to the smallest opening. The other difference that I'm aware of is that the AIS lenses tell the FA and others with program mode, what the focal length is (at least for fixed-focal lengths, I can't say that I know about whether zooms do or not) so that the camera can maintain a faster shutter speed for lenses 135mm and longer, when in program mode.
Some claim that the Nikkor 28mm f2.8 AIS lens is one of the finest that Nikon designed and produced. I can't comment on it as I have not tested it against other 28mm lenses nor do I own it, but the reputation certainly continues to prop the price of that lens on places like the 'bay. It's considered a cult object, like the 180mm f2.8, the 35mm f1.4, the 200mm f2.0, and some others.