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Nothing like being able to spew molten rock from your mouth, have it solidify rapidly and fill a room with acidic mist.
Sure, Kakashi's lightning nature does have it's perks in this fight, bearing that one of Mei's natures is Earth. But, that being said, she also has a greater effect on the battle field, being able to change the topography to suit her needs.
Now, her standard techs, the fire,water, and earth ones will be susceptible to Kakashi's Copy, but it will depend on his ability to use them. Remember, Sharingan, and MS even more so, amount to a HUGE drain on Kakashi's chakra. It does give him an edge, but it also forces him try to end fights quicker. If he can't get the first Kamui off, chance are he won't try it again. In a fast-paced, long range ninjutsu battle, he can't risk wasting more than he can.
Now, we haven't seen any real fighting done by Mei save for the bout with Sasuke, leaving a big information hole. However, it can be assumed based on her title as Mizukage that she is the strongest and smartest(best fit to rule) from the Hidden Rain. Kakashi has been offered the position, but only after the 5th Hokage was in a coma, and the "6th" Hokage, the Leader of ROOT Danzo, had been killed by Susuke. His appointment was more of an attempt to fill a power-vacuum left in the Hidden Leaf.
So there it is. There is my personal explanation as to why I feel Mei would win in an actual fight between the two of them. No Plot-no-Jutsu, no Insta-kill Kamui snipe from across the field, a true fight between shinobi.
Good day.