As a current manual driver and manual enthusiast (I guess), I would say I would want the 6 speed. The M5 to me is a great car on the road, but I dont think I would take it around the track. I enjoy rowing through the gears too much myself to let that go. If this were an M3 on the other hand, I would probably take it to the track occasionally. Being as that is the case, I would probably take the SMG.
Now, if the car were to be tracked or autocrossed regularly, I would without a doubt go with SMG (as long as it is on the M-models and not the SSG previously offered on non-M E46's). If it was a car to go around town, I would probably go with the 6 speed.