Ok.. gotta jump in here...
Boxer engines, along with Inline 6cyls and V12s are naturally balanced motors. Very smooth! I found a great article a long time ago that goes into a fair bit of detail about what motors are balanced and such. I liked it enough, I scraped it from the site, and put it on my server. Her is the link.
http://www.aphkac.com/automotive/tec...ce/smooth1.htm
And specifically, for the Boxer engine.
http://www.aphkac.com/automotive/tec...ce/smooth5.htm
The rough idle issue some (including myself) notice, could be a result of rotational mass. The flywheel holds energy, and if its RPM changes, even just a little bit, you'll feel it in your car. Kinda like when you blip the gas, the car shakes.
Just my .02c worth.