The SMG have their own sets of problem. The simpler 6-spd would be the wise and fun choice. Even with all these potential weaknesses, the S54 is still a hell of an engine and loads of fun to drive.

FYI...the S65 in the e90 M3 also have the rod bearing wear issue along with their own sets of problems. My point is that all M cars required a lot of upkeep. Whatever budget you have for the car, factor in another 30% or more for maintenance.