Tranny will get better after a few thousand miles, but will never be Porsche smooth. Even Honda manuals are notchy on the 1-2 shift, but less than BMW for sure. And all Tremecs are quite notchy too. Nature of the beast.
Bottom line is you'll always have to devote more time to the 1-2 shift (milliseconds more). Don't rush it and you'll never have an issue. Not a big deal at all for most of us. If you want the quickest shifting time, should have gotten a DCT. But the pleasure of driving a manual is well worth is unless you're racing competitively IMO.
Even with its idiosyncrasies, I rate the M3 a 9 out of 10 (10 being best available, not perfect), just behind Porsche (10). And the M3 has better feel than Porsche, which feels rubbery as hell, but still precise. After switching to RP Synchromax fluid, I'd actually give it a 9.5, due to that slight notchiness in 2nd and 5th. Those wanting quick shifts might rate it lower, but that doesn't bother me. Good day.