Kakashi was caught by the element of surprise. I think this Kakashi Vs Pain fight could single handedly remdeem the Naruto series. Yeah we know that the Rinnengan is the most powerful eye of the three, but then how much does stuff like this matter when you are hitting the heights of great fighters? Madara had EMS and still lost to the First.

I think that Kakashi, coupled with his MS, could do some damage here. Why? Because Kakashi is supposed to be a genius without the Sharingan, whereas Pain just has an uber power up. Unless Pain can just nulify attacks, disrupt his opponenets internal chakra or just time travel, this could be a good fight.

Things against Kakashi right now are his low chakra/stamina level, and the fact that Jiraiya lost against Pain.