The Gen 1 factory exhaust was a smaller diameter, IIRC. So the Magnaflow kit for the Gen 1's increased to 2.25" which helped in the performance increase. I remember seeing some older threads (about 2 - 4 years ago) that the prototype for the Gen 2 didn't provide any substantial performance increase, which is why Magnaflow delayed in manufacturing the cat-back system for Gen 2's.
Tony from LLSOC had the prototype from Magnaflow on his 2006. Maybe they made some changes to the kit to give it more than just a 5 hp boost. Although, if they are showing the Gen 1 performance numbers for the 16678 Gen 2 kit, chances are they haven't.
Still, I'll be ponying up for an entire kit next year. You've all convinced me that it's better than stock, which is all I have right now. There's no way I can sneak that one AND summer wheels/tires/tinting/rotor pros past the wife, so they'll have to wait until next year.
Tru