The front suspension.
The 3rd Generation has the TTB where 98+ is an IFS suspension. Basically the IFS has less travel which therefore decreases flex. Great for driving on smooth roads, not so great of the beaten path.
Also I know the 3rd Generations its easier to swap to manual locking hubs, over the automatics that tend to blow up when you need them the most. I am not so sure about the 98+. I know for a while they had vacuum hubs that would suck pretty bad, but i think they have a kit to fix that. As far as the rest of the truck is concerned, they are all pretty much the same. Except around 2001 they changed the 4.0 to SOHC motor instead of the OHV. The new 4.0's have more HP & Torque, but also at a higher RPM (not what you necessarily need for off roading)