He was probably tired, I mean he had been fighting for long and Kakashi had been give a chakra cloak before the battle, Obito could have raped with Mokuton imo
a couple of times? no it was once and it was only because Naruto forced Obito into using Intangibility and so what? withought Naruto's assistance Obito also could have killed Kakashi multiples times before that fight too.
Whatever man, Kishi made parallel between the 2, he showed them as rivals fighting to the death, which is why he compared them as kids and now. It's why kishi restricted kamui and put them both in the kamui dimension. And kishi did it perfectly, he showed who the superior shinobi was, Taijutsu Kakashi was always better, Ninjutsu - Kakashi has over a thousand, and Obito's genjutsu won't work on Kakashi (it wouoldn't make sense anyway considering they have the same eyes).
And if you can't see that and just blame it on plot or handicaps then you obviously don't understand what kishi was trying to portray in that fight. In that case keep telling yourself otherwise, I don't really care because I read the manga and saw a winner of a fight of 2 powerful individuals fighting a fair fight.