This question has become more complex.
If it was the M3 with DCT vs. the 997S we have all come to know and love the edge in a straight line goes to the M3. Around a track it really comes down to the driver that can best extract his cars abilities, but the 997 is a bit more at home here. Either way, the M3 has the more technically impressive engine and tranny.
The 997 is getting a facelift for August delivery. The changes are direct injection, boosting power to 380 hp and PDK (porsche dual clutch). There are also minor cosmetic changes (LED's and junk). With these upgrades the 997S regains the upper hand and it does not seem so difficult to choose a 997S over an M3 anymore.