I've not ridden the F so can only comment on the naked and mine handles just as well as my K5 gsxr1000 did,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.
On a side note i recently found out that M4 has a full exhaust system for the Gixxes 1000, anyone here run that full exhaust