One issue that is being overlooked when comparing increasing the displacement of a 3.2 to 3.6L vs the 3.6 motor from Porsche, other than Jake's modifications fixing some of the weaknesses of the motor that keep some people up a night and not having to worry about converting to a 7.8DME on the earlier cars, is that the benifits of the variocam plus system on the factory option.
The variable valve lift and increased variable valve timing (at least when comparing to earlier 3.2 motors that use a 7.2 DME) provides substantial benefits on a street driven car. Variocam plus both increases fuel efficiency, throttle response, drivability and performance (essentially two cam profiles in 1) when compared to an engine of similar displacement not using the variocam plus system. Obviously at full throttle and load on the track, both engines will have similar performance all else being equal.
Oh and my 3.6 X51 puts down more than 300 rwhp with stock programming
Anyway, I'm sure for most people Jake's option makes a lot more sense, but at least I can go to 3.8 or more starting from my engine if I ever have an issue
-Todd