I think that Tobi uses Kamui, that is why he was able to stop Kakashi using it and it is why Kakashi said at the end "I though you use two jutsus...but you only use one!" Kakashi was able to recognize that it's Kamui. Kakashi even said, "I haven't met anyone yet who could stop Kamui." But Tobi did. Also, as far as we know, Kakashi himself doesn't know or recognize many other transportation jutsus (other then summoning and thunder god).
Tobi also said "I see Kakashi you sent Naruto's rasengan to the other dimension". That other dimension is where Tobi goes between S/T uses and where Kakashi sends things with Kamui. Which means Tobi uses Kamui on himself to teleport, which explains why he needs to materialize in order to teleport.
This is why when Tobi tried to absorb Naruto the sharingan was able to hit Tobi. Kakashi sent Naruto's sharingan to the other dimension, Tobi has to materialize to use Kamui, and the portal to the other dimension was opened, allowing the Rasengan to come through and hit Tobi. Why are there two seperate jutsus doing the same thing? because there aren't two different jutsus that do that. It's only one jutsu. Kamui.
I am not currently supporting the Tobi=Obito theory. To be honest it would be cool but I have my own reservations. However, I do understand that this theory can lead others to continue to assert that Tobi is Obito. Then again it could just be two Sharingans that do the same thing, like how Itachi, Sasuke, and Madara can all summon Susanoo but it's suppose to be a rare technique among the Uchiha.