if you look into the history of the 996, it's really an amazing technical leap for Porsche, but it's clear that it took awhile to iron out the bugs, and the bugs still persisted a little bit in the 997 series. the M96 powerplant has something like 17 technical volumes (the M64 had about 3-5) for the running updates to everything from the cooling system to the RMS.
in the 997s with the latest DI engine, not only is the engine lighter, but it's stiffer and is a design evolution that bypasses some of the 996 teething problems.
that's not to say that all 996s have issues, but 10% failure rates on the RMSs were what my local dealership reported. Porsche is great about covering them under warranty, though.
my vote would be for a 997, not a 996.