In 96, there was a significant change in the rear driveshaft, specifically the design of the slip yoke. The later ones are said to be more prone to vibration. I have not noticed this between my 95 and 99, but it is a very different driveshaft.
A very big improvement was made in 97 in the location of the anchor points for the parking brake cables, no big deal if you drive an auto but a big hairy deal for us stick shifters. The 99 parking brake actually works.
The later interior has less storage than the earlier ones, if that is possible. Gone is the little shelf below the glove compartment, and some of the little recesses in the console, and the big ash tray. The instrument panel is redesigned, in part for the passenger side airbags, and there is less space to mount any additional switches or other gadgets. The power window and lock switches on the later ones are better placed, the console box is smaller but now designed for CD's, and fairly functional cup holders are now cast into the console (they moved the brake lever sideways a bit for this). The later interior looks a little more updated, less like something designed by AMC in 1984, if that's something you care about.
There was a seat and steering column change in 95 when they got driver side airbags. The later seats are still all right, but in my opinion they are not quite as nice as the deluxe version of the old ones, and there is no option for the tilting base. The steering column and its controls on the 95 were a step down, with a really lousy wiper control that makes it common to accidentally actuate the wipers when signalling turns, and horn buttons that never seem to be where you need them. The 99 has yet another generation of controls, presumably introduced in 97, which is better laid out, though for some unaccountable reason, both lack a single-wipe position, which I miss.