Everyone has an opinion, including me!
A friend and I took a rented E46 SMG and my E90 DCT on some of Malibu's finest roads several years ago. The E46 was the more rewarding canyon car of the two because it was more communicative and its power peaked lower in the rev range. Curiously, the E90 M3 seemed to me to least interesting in the canyons and best in the city or at the track. In the city, the E90 could really calm down and coddle. On the track, the S65 engine does its best work and the E90 chassis comes alive and communicates.
I wrote a blog piece on the two cars
here.
In my eyes, the E46 is the quintessential M3. The E90, on the other hand, shines because it has the best M3 engine.