I have a '11 990, and I felt just as you do when I first bought it. Missed shifts everywhere, notchy and weird false neutrals between 4-5.
I'd say give it some more time to break in, mine seemed to smooth itself out over time. Haven't had a false neutral in a while, and missed shifts are less than 10% of the time.
I've had (quite a few actually) bikes with smoother tranny's but this one grew on me over time.