Itachi didn't have MS at the time and Kakashi just has more experience and probably a much larger jutsu arsenal even at that point. So he would probably win with mid difficulty at most
How was Kakashi able to warp right at the spot where obito was lying? Can he teleport himself back and forth across a wide area? Also how did he know Obito was at that spot in the first place?
http://narutobase.net/manga/Naruto/655/5
I guess it could be plot but couldn't he also just be getting better at chakra control with it? Also sasuke was going blind with MS but maybe Susano'o and enton/amaterasu just strain the eye more than kamui. Just a thought