I think I can help you here... Well, hopefully.
I'm the proud owner of a 2004 996 GT3 and a 2008 E93 M3. Only my M3 isn't exactly stock. The previous owner put the RS46 Stroker Motor package from RD Sport in California and changed out the differential. The car is pretty sick and the torque is amazing.. (400+ ft/lb) It's a DCT.
I use the two cars for completely different things though. The GT3 is my track car and is set up that way. The M3 is my everyday street car. The GT3 in my opinion is a much better track car than my M3 even with all of the power that the M3 has. (Too heavy, convertible). The M3 is just so comfortable and a joy to ride on the street. I'm coming from a E46 M3 (6MT) and an E36 M3 (6MT) before that so I'm pretty familiar with BMW. (And for those of you wondering, I would never buy a 335!! It's just a different vehicle all together. M Power baby!!) The GT3 is a much "rougher ride" although the 997 GT3 is much more street friendly.
So I guess it comes down what will your primary purpose for the car be? The 997 GT3 is a much better car for the street than the 996 GT3 IMO and is also great track car. I've been contemplating selling both for a 997 GT3 myself. But I think what I'm going to do is wait a year or two and get a 2010 GT3 to replace both
Hope this helps