I might as well chime in here with a few points about SMG, since I've had mine for 5 years and I have 214,000km on it.
The SMG pump problem is somewhat of a known issue for sure but what you spend on a pump you save on a clutch. I track my car a lot, have been for 4 years or so, and finally I needed a clutch replacement (so I thought). Original clutch, 199,000km, and it still had life left when Rocco @ RMP took a look at it. I replaced it anyway but I could have gotten another 80k - 100k off of it. SMG saves your clutch bigtime because it is MUCH better at shifting than any human is. Unless of course you keep using launch control and burnout mode, but that's going to wear the clutch the same as any manual. I never use either simply because it's pointless, I am not a drag racer, and don't feel the need to impress anyone.
The reason I thought it needed a clutch replacement was because of slipping but turns out it was my SMG pump. I have a new one on order now. I don't know how people are getting pumps for $800 but I am getting mine for $1900 from Tischer. $800 for a used pump perhaps but there are a slew of horror stories on M3F about used pumps. Don't do it. Labor is going to be $600 if I decide not to do it myself (which I probably will since I have the AE software and can do a bleeding). Swapping the pump out is actually pretty easy from what I've read with the exception of the hydraulic lines which sometimes need a torch to get them out. Not looking forward to that but we'll see how it goes. I'll let you know
Anyone who says SMG shifts rough has either not driven one or not driven one properly. It does take getting used to and you have to time your lift of the throttle and the severity of the lift based on the mode you are in as well as the RPM. Took me a solid 2-3 months to get used to it but after that shifting was VERY smooth. Same with the automated mode, you eventually learn when the car is going to shift and learn when to lift. You can even tell the SMG to shift in auto by lifting the throttle at the right time. It's a pretty slick system. On the track it's absolutely awesome. It shifts faster than any human can (no matter what some people say) and feels incredible in S6 mode. It also won't let you do the dreaded money shift which is nice
There's really no other issues with SMG other than the pump and the infamous salmon relay (a $7 part which takes 30 seconds to replace and I guarantee you will be replacing it at some point). Actuator and transmission failures are MUCH more rare. I've actually only seen one transmission replacement posted on M3F. Thank god, because it's $7k for the tranny alone (same as 6MT really).
In summary, the added cost really isn't going to impact you if you can afford to maintain an M3 to begin with. As I've said to many others, buying an M3 is easy, maintenance is the expensive part, 6MT or SMG. Especially if you track it. What's nice about getting the SMG is you know the clutch is going to be fine unless the previous owner was a knob and used the LC a lot. Same could be said of 6MT though, and with the 6MT the clutch is very likely to be worse because of human imprecision.