sources like car mags seem to regularly describe the e90 M3a the greatest of all time. Having owned multiple BMWs and 3 M cars and driven every type of M3, I agree. The driving feel may be different between them, but any claim that the e46 is better or more involving is mostly just nostalgia.
Just got done with my first track day in my E90 and it was quite simply the most incredible and connected I have ever felt with a car. It may be smoother, but it does what you want it to, when you want it to, with an almost telepathic immediacy. Just spectacular.