The whole point is that Mokuton and Zetsus are made from elements that are disadvantageous against raiton element, perhaps to the point, that it might be even easier to kill using Raiton against them, than a normal humans.
Obito is only able to do small-scale Mokutoun, through which Kakashi would cut through with his Raikiri/Raiton element like if they were nothing more than leafs. That's why Obito chose to fight him using Taijutsu and Fire element... although, the Fire element could have been countered by Kakashi's water jutsu easily and in a taijutsu fight, Kakashi is simply superior.
That is, Kakashi is really the worst enemy Obito could have gotten. The only reason he was able to kick Kakashi's ass before, was thanks to his Kamui, which is really an overpowered jutsu in his hands, but the moment that was taken care off, the roles have switched.
The only thing worth considering, is if Obito really was unable to hit Kakashi's vitals at that clash, or just chose (subconsciously) not to. Otherwise, his ass was kicked, or it would have been a draw at best. Of course, if he still had his advantage of Kamui over Kakashi, then Kakashi would have lost in a one on one, as it was shown when they battled in the Impure World.