The L98 engine was an iron block and Iron head conventional engine design. Other small black parts were interchangable with it.
THe LT1 came along and it was the 1st step away from the conventional small block engine. Came with reverse cooled heads (GM got in trouble for using it on the LT1's and i believe thats part of the reason they aren't used on the LS1). Lets the heads get the cooler flow side of the coolant first allowing the engine to rev higher and still keep the internal cool in the vital spots. With out it the LT1 cant rev as high. A new ignition system (not bad just in a bad spot).
For the LS1, Gm took some old school ideas from some Ford heads and built on them. Producing a set of heads that had a higher flow and higher velocity. Comparibable to a LT1 would get out of a standard performance port and polish. The Heads aren't reverse cooled. The entire block and heads are aluminum. The air take is made out of BASF Plastic's and throws off a lot of heat. These are some of the reasons the LS1 can rev higher stock for stock against an LT1 without reverse cooling heads. Different ignition system 1 coil pack per cylinder. The LS1 comes with a lot of things the LT1 guys have to do. Something like 60% better air flow through the intake (more of direct shot), monoblade throttle body so no need for an airfoil, lighter/better intake manifold, comes with 1.7 rockers, awesome flowing heads, aluminum drive shaft, dual piston brakes..
Whats great about an LS1 set up is that the weak points (powerwise) lie in the camshaft profile and the exhaust. You change those two and your looking at 400wrhp.
But you have to remember that the LT1 is 11 years old design. It was the rave back then like the LS1 is the rave now.