What I've heard (and this is all hearsay) is that the fairings and the windscreen plant the faired version's front wheel more solidly at high speeds through turns, and I'm kinda willing to believe that, but I think that it's minimal at best.
I think that the faired looks better in blue, and that the naked looks better in red. The faired in red looks like Angry Birds to me. I'm kinda an outlier though as I don't own my own yet.
“Give a man a fire and he's warm for a day, but set fire to him and he's warm for the rest of his life.” - Terry Pratchett