Get the 6 speed!

 

Both are really fun to drive but my nod goes for the stick all the way. There is no doubt you feel more connected.

 

I have owned 2 M3's, both of them are stick. 3 of my friends have M3's with SMG. SMG is great, but IMO I find it slightly more tedious. Less involvment. The whole thing about it shifting faster is irrelevant, it comes down to the driver. I have been able to pull slightly or be even with my friends that drive SMG. I drive my car all day long, even in traffic, and it's like second nature to me, very easy to drive around town even in traffic. The 6 speed has a great gear box! I would be careful with a used SMG M3 the first generation SMG's had some problems. It really comes down to personal preference. I would only bo stick. We even have a new M6 in stick.
"Real men use 3 pedals"

 

6 speed. i love it and dont think i would ever want anthing without a clutch if its a small sports car or exotic.

 

I like the SMG III a lot more than manual but since they don't offer that in the M3, I'm going to recommend the 6speed to you. SMG II is way too unstable and shaky from what I've experienced...