[james0246]

^That doesn't actually prove that Madara/Tobi's eye is, or should I say was, Obito's eye. Madara has extensive knowledge of the MS, Sharingan, and the techniques it posses. He has shown this knowledge by somehow dispelling (or at least negating) Amaterasu; explaining the difference between a complete and incomplete Susano’o (as well as mentioning how rare it is for the technique to appear at all); and he has explained several ultimate attacks that the Sharingan posses (Shisui's mind-control, and the recently revealed Izanagi). So, it stands to reason that, even after only hearing of Kakashi's technique, he could already know of its presence within the pantheon of Sharingan techniques (i.e., while not "common", it is still known). We must recall that Madara, more or less, invented the Mangekyo Sharingan, so he would know best about the mutated eye.

(I should point out now, even if just as a quibble, Sasuke and Itachi's eyes are reversed - their Amaterasu and Tsukuyomi come out of different eyes; I don't know if that necessarily negates your theory (it does, somewhat, for Itachi and Sasuke, but not necessarily for Obito's potential 2nd eye), but it does show that the basic pattern (EoD - left, EoU - right) doesn't carry through from person to person (though there is always a separation (left and right eye each contain one known technique, and both can be used for another technique (and 4 eyes can be used for a 4th technique)).)

That being said, Madara’s technique, and Kakashi’s Kamui are too similar to really be classified as different techniques (they both, essentially, do the same thing (transport matter from one place to another), but Madara is able to more accurately and adequately use his technique.

Additionally, since the MS grants one supreme Ninjutsu, and one supreme Genjutsu, Obito’s other eye, wherever it is, should be a genjutsu eye, not a Ninjutsu eye (since Kakashi already has the ninjutsu eye).

(Also, I should mention that it is still unknown if Madara is even using his MS when using his technique. It could be possible that his Time/Space thingy is actually simply a Sharingan technique ala Izanagi, and that is why he retains so many Sharingans...)

To expand further, though, the negation of powers seems a bit of a stretch. Tsukuyomi does not negate Amaterasu (no, Sasuke using his Tsukuyomi eye to dispel Amaterasu was not a form of negation, he could simply control the Amaterasu flame with his non-Amaterasu eye), nor does whatever Madara/Tobi (if it is a MS technique) does negate Kamui. If they are connected eyes, it wouldn't be that the one eye negates the other; it would be that one eye is simply more powerful than the other. In fact, at least for Sasuke and Itachi, Madara/Tobi already explained that each brother was more geared toward a specific eye, and, consequently, that eye was significantly more powerful than the other - Sasuke's Tsukuyomi sucked (only lasting seconds, and not being able to create "dimensions" within the mind), whereas his Amaterasu comes with a slew of secondary techniques (his Enton attacks); but Itachi's eyes were the exact opposite, with an uber-powerful Tsukuyomi (able to create entire realities within the victims mind), and a, I'll say, average Amaterasu. So, between the brothers, one eye is more powerful than the other, and that eye would, for lack of a better description, kick the weaker eye's "ass". Consequently, if Madara/Tobi's eye is the brother to Kakashi's eye, then it isn't that one power negates the other, but rather that one eye is simply more powerful, and if your hypothesis is correct, the stronger eye would be Madara's eye.

btw, how does 486, page 04-05 prove that Madara only has one eye?