If you mean the pros of the Raven model to the 'standard' colors... purely cosmetic with black fairings and red pinstripe on the wheels.
Overall for the R6, if you can find one, try to get the 2005 model instead, it has better brakes (including Brembo master cylinder) and inverted forks. The '05 model was pretty much the best year for the second-gen R6... The newer R6s models are the same bike, but I believe did go back to the '03-04 specs to keep the price down.