This is a pretty chronic problem with the 6 speed. It took me months to get used to it, and I still crunch it once in a while. This was discussed a while ago on the forum and the consensus is that it's pretty normal and tends to get a little better over time. Not sure if that means it's the driver or the transmission that's improving, though.
I don't think the 'drive-by-wire' has anything to do with it.