Drove both and went with M-DCT as I felt it is better matched to the motor.
I also own a gated 5MT and another 6MT, so I wasn't too worried about not getting my MT fix.
I really don't think you can go wrong with these S65-powered M3s - just get what you like!
BMW: 2011 AW/Black E92 M3 DCT - 2010 BSM/Tan E90 335i AT
Other: 2004 AW GDB STi 6spd - 1991 Nero/Nero 348tb 5spd