A lot of people are underestimating Kakashi here. Let's examine the facts about Kakashi:
1. Graduated from Ninja Academy at age 5
2. Became A Chuunin at age 6
3. Became a Jonin at age 11, also gained the Sharingan during this time
4. Was in ANBU at a young age (forget when he joined)
5. Because of his Sharingan, Kakashi has master 100's of jutsu
6. Has done battle with and lived through S-Class Ninja. People might say that he was was on par with Zabuza (who is now considered weak compared to where we currently are in the story), but you must remember that Zabuza was also considered a famous/legendary ninja as well (which is why Kabuto revived him).
7. Kakashi's prowess only increased during part 2.
I'm going to be frank here. The only reason Obito has the upperhand on Kakashi is because of a few factors:
1. Rinnegan-- If he didn't steal that from Nagato, he would have been toast.
2. Kakashi did battle with the Edo-Jinchuriki, has been battling all day and has yet to sleep or eat. I am pretty damn sure he is exhausted. Obito has not done too much fighting yet. A couple clashes with Naruto, a couple clashes with Gai/Kakashi and a couple of clashes with the alliance. He hasn't done much yet, so his chakra reserve is up.
3. Kakashi idolized Obito, looked up to him and thought very highly of him. Kakashi is still trying to come to terms that Obito is a villain now. If you really think about it, Kakashi is going easy on Obito. Look at all the battles Kakashi has been through and compare it to this one. Kakashi doesn't want to fight or end Obito.
4. Kakashi had to figure out how Kamui worked. Once he got that figured out, it was easy for them to devise a plan to defeat Obito. Again, Kakashi can defeat Obito, he just wants answers.
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Kakashi is just downplaying is abilities right now because he still cares for his former friend. He could have easily killed Obito right then and there.
Obito has never been above Madara, the Kages, etc... etc... the only reason people feared him is because they thought he was Madara. Do you really think Obito would be where he is at today if he went around as himself? People would have thought of him as a joke. He would have gotten no where. He and Kakashi are on the same level just about.
-Obito could not defeat Itachi, just as Kakashi could not. Why do you think he did what Itachi asked? Obito knew he couldn't defeat Itachi.
-Obito could not defeat Pain, just as Kakashi could not.
-He was easily defeated by Minato:
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-He could have been killed by Konan, if he did not think quickly:
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If Konan blew off his non-Zetzu side, he would have been dead
In short: Kakashi and Obito are on the same level. I will be honest... Obito MIGHT be a little stronger because of his Rinnegan, but that's all.
-Obito has MS. Kakashi has MS.
-Obito has Kamui. Kakashi has Kamui.
-Obito has Senju DNA on the right side of his body, which gives him the ability to regenerate that side. Kakashi is holding back because he doesn't want to hurt Obito. If Kakashi got serious and attacked Obito's left side, Obito would be in trobule.