Actually - I don't think there is much of any difference in paint quality. BMW has just as much orange peel as the GT-R. GT-R's paint may be a tad softer though. Interior wise - I like the layout of the M3 better and the bits/pieces look at bit nicer but the M3 doesn't have any leather on the dash either. I wouldn't let the interior drive my decision here. The GT-R isn't anywhere near Corvette bad.
I think all you have left out are the mechanical noises and perhaps some ride quality compromises that you get with the GT-R. My research has indicated that some of those issues can be remedied (sp?) with non runflat tires and the mechanical noises aren't that bad with upgraded tranny fluid????
The GT-R will be more expensive to maintain but I really don't think it is as much of a delta as you think.
The GT-R has really grown on me in the looks dept. Also think it looks much better in person than in photos. It will definitely garner more gawks than the M3 if that is something that is important.
For your intended use I'd give the GT-R much consideration. What have you been driving and what are you accustomed to? American, Euro, Japanese, British,..? I think that may play a role in which one you will like better as well.