A few other items worth mentioning:
1. Intake: Thermosplastic intake being separated from the hot coolant allows the air going inside the engine to stay cooler, which is a good thing. Colder air = denser air. Intake replacement job is much easier now and less messy.
2. Heads: This is where the magic happens! Everyone has probably heard about the high-flow LS heads. Except for the short-lived cast-iron heads of the very early 99-00 LQ4s, all LS heads were aluminum and had incredible factory airflow CFMs for the time. More airflow = more power. What is so special about that 15 degree valve? This was the early era of advanced computers using new technology such as Advanced Finite Element Modeling (FEA) analysis. The different variations and head compatibility across the production run is insane if you are looking for budget high performance heads. Aftermarket heads push the limits even higher. Also, the head bolt threads being deep into the block helps with strength and reduces cylinder distortion when the heads are torqued down.
3. Camshaft: The larger base circle of the camshaft allowed for a more "tamed" engine permitting a larger lift and more duration. Basically, the engine can idle smoother even though a larger profile cam is used because the cam ramps are more gradual. Also, the camshaft is hollow, allowing for less rotational inertia and higher RPM performance.
4. Oil pump: Gerotor oil pump is driven off the crankshaft snout instead of the camshaft rear gear. This relieves stress off the camshaft allowing for higher RPM range. The cam does not have to deal with the load required to pump oil pressure.
5. Injectors: According to the author, the injector technology was nowhere near what it is today back in the early 1990s when under development. So the system was designed around the best injector design at that point. Again, later injectors as the higher performance engines came out offers great compatibility with any other LS engine, with only minor modifications required.
6. The cast aluminum engine covers (oil pan, front cover, rear cover and valley cover) being part of the structural integrity of the block is also probably worth mentioning. This helps with the noise, vibration and harshness (NVH). The gasket technology is also a plus, although eventually gaskets still leak with high mileage and age.
Here's a good video on all the RPO variations: