Well, that's exactly the reason Kakashi won't get himself killed again by a Rinnegan user.
"The same trick won't work on me twice".
Ever since Kakashi said this, he was never beaten twice by the same jutsu/trick. He already has experience fighting a Rinnegan user and his genius is enough to use this experience to his advantage.
True, he has his strengths but so does Kakashi. Namely, Kakashi is faster, more intelligent, physically stronger, more proficient in ninjutsu and generally a more versatile ninja.
Actually, Obito can use Kamui, but it would be risky for him, since if he turned intangible his body parts would appear in the real dimension and could be attacked. Also, it's possible that Obito can nullify Kakashi's Kamui, but we are not 100% sure of this. Kakashi might still find Kamui useful for example for defense.