The 6MT in the M3 is less than wonderful in a variety of ways. Not just the clutch engagement but also notchiness and grinding in 1st to 2nd shifts. For everything that the car does so damn well, it always surprised me how BMW implemented the 6MT. Just drive a Porsche for 15 minutes and you will know exactly how a manual tranny should be implemented. One of my few complaints about the car as well.
This isn't to say the 6MT is a "bad" 6MT as much as it is me saying it is NOT up to the same standard as the rest of the car and therefore takes away some of the enjoyment of it
Like I said, not necessarily a "bad" tranny but far from a stellar one on a car that is otherwise pretty damn stellar. For me, the only real negative of the M3 is the weight, the notchiness and feel of the 6MT and... well, that was about it.
IMO, if BMW is going to offer a 6MT they should offer one that performs like you find in a Porsche... now that is a 6MT to enjoy.