http://www.ninjette.org/forums/showt...534#post809534 has a bunch of EX500 suspension details.
The Gen2 EX500 fork springs are a little stiffer than the NewGen's, but according to RaceTech's calculator, they're correct for a rider of about 50lbs. Even for a 100lb rider, they suggest 10% stiffer than the EX500 springs; for a 150lb rider, they suggest 25% stiffer. If you have some laying around that you can just toss in, they're less bad, but they're still below the proper rate for any adult. I would only put the tiniest amount of money or effort into acquiring EX500 springs as an upgrade, and only if I were very small. Getting the wrong parts for slightly cheaper isn't really much of a deal when you can just spend a little more on springs with the optimal rate.
The EX500 shock is pretty similar to the PreGen's, except that it has preload adjustment and a much softer spring, 300# vs. 440#. The NewGen's spring is about 520# for some comparison. I doubt the shock itself is much/any better than the PreGen's other than being able to adjust the preload, since it looks nearly identical. Looking at RaceTech's calculator again, the stock NewGen rear spring is a bit stiff, good for about 220lbs. The PreGen's 440# spring is good for about 140lb on the NewGen, and the EX500's 300# is below the minimum 31lb the calculator will accept.
RaceTech's calculator points out a good chunk of the problem with the NewGen's suspension. The rear spring is good for a 220lb rider, but they recommend 25% stiffer fork springs for a 31lb rider (the lowest number it will take). You need 90% stiffer (yes, almost double) fork springs to match the rear spring. The Ninja 650 is oddly sprung like this as well, but with the fork springs about double what the rear spring can handle. The EX500 is just soft on both ends (but more on the front). It really blows my mind that Kawasaki does such a poor job of choosing spring rates.