Kakashi was the only person apart from Naruto (who was Pain's target) that Pain decided to attack with more than one path.
Pain was afraid that his strongest body, Deva, who could keep up with 6-tailed Naruto, was not enough to handle Kakashi.
But now Kakashi is a league above what he was in the pain arc.
The difference in power between Deva and other of Pain's paths is huge. Kakashi can warp away Deva and the reviving path at the beginning. We know he is capable of two consecutive Kamui shots of about human size, as he has shown against Sasuke's susanoo arrows.
It is at this point that Kakashi is endangered the most - four paths remain and Kakashi's movement will likely be handicapped to some extent due to two such fast Kamui. This is Pain's best chance to get him, but actually, Kakashi doesn't have to kamui two bodies at the same time.
If he warps just Deva, he won't feel any side-effects of Kamui. Then, after holding the remaining 5 paths for a moment (which will be easy to do with doton walls, travelling underground and bunshin feints) he can use another Kamui on the reviving path. This way he won't leave himself open for attack at any point, because two non-consecutive Kamui is not enough to exhaust him.
Still, even with all his improvement and intel, Kakashi won't be able to handle them easier than high difficulty.