The above video compares a top of the line sample of the E90 with a very bad crappy sample of the E46. How about an apples to apples comparison with both cars being comp package, 6spd etc.
No doubt E90 is the superior car, faster, more powerfull, no question about it, but as most reasonable ppl in this thread have pointed out, the E90 is def lacking that raw race car feel that the M3 has managed to maintain with the E46 body and imo that makes the E46 a more fun car to drive. The E90 has gone the route of big engine in a huge car.
Here is an interesing video, enjoy.