I've had a lot of time with the e46 and e92 and currently own a 2010 GT-R.
If it's a weekend driver for you and the badge doesn't bother you, hands down GT-R smokes the M3 in every possible performance category and that's coming from a guy who originally thought he'd never buy and $80,000 Nissan and had preordered a 2008 M3 at the end of 2006. The GT-R is as close to the world of exotic sports cars one can go without truly entering into the Ferrari, Lamborghini, etc. from performance and rarity.
On the flip side, GT-R paint quality is as poor as all Nissans. All Nissans including GT-R's, have that typical "orange peel" paint job with super soft paint that scratches when you look at it. Don't be fooled by the special super silver $3000 paint. The transmission gets louder over time and of course unlike your BMW, maintenance with the Nissan it's on you. Nissan does have free services on the GT-R that are performed at certain time intervals, but it does not cover oil changes. I only have 3000 miles on mine and don't drive my cars very hard, so I have not experienced personally any of the horrible maintenance stories that are floating around out there.
As a heads up, you may be able to pick up a brand new 2010 GT-R for marginally more than what your friend is willing to part with his. Dealerships can't move them right now and are willing to deal to get rid of them because of their cost to floor plan.
Fun car, turns heads, and if you don't need the four doors yet go for it. You only live once. Let me know what you decide.