it's been reduced 2 decibels.
from 98 to 96.
generally this is almost untracable to the human ear so as spectators/racers we aren't gonna hear any difference.
However an actual reduction of 2 decibals can make a decent impact on power output of a bike so the twin pipe design, in honda's eyes, was worth the effort to increase power 'slightly' over the 05 and still keep it in line with various governing bodies ever changing sound restrictions.
as for handling, As far as I am aware this was not in anyway Honda's motivation for the design and did infact ditch an early twin pipe design because it was having a negative effect on handling. basically it's been done to reduce decibels whilst maintaining power and handling properties found in the 05 bike.
I tried an 06 this past sunday. it still handles great, it still has a nice smooth power output and doesn't sound any different.