Just saying this right now but these are NOT theories due to the fact I have little evidence, if any, to support them and therefore am just posting them as something interesting to think about/take into consideration and raise a few questions.
1) Uchiha Madara's Missing Eye's
First off when i talk about Madara i am referring to the Edo Tensei version not Tobi.
Now there are many questions that have been raised since Madara was resurrected; Who Tobi really is, How/When did Madara really die if not against the 1st Hokage (obviously knew of Nagato), ect.
But one i feel like is commonly not noticed is where are Madara's eyes? Are Madara's eyes (right now, as an Edo Tensei) really his original? Some will argue that they are since he can use his EMS as well as the Rinnegan. Remember though that it has been stated the resurrections can use all of their original abilities. (http://www.mangareader.net/naruto/520/13) (read next page too, says how they can still use sharingan/rinnegan)
Also compare and contrast Itachi and Madara: two http://www.mangareader.net/naruto/549/6 http://www.mangareader.net/naruto/560/2
Notice how both of their eyes are black? Itachi's eyes were obviously taken from him and given to Sauske, but i feel like the black eyes mean they are not the originals eyes for the Edo tensei, meaning that before Madara died he gave them away. My only guess would be that he gave them to Nagato somehow (considering he knew of Nagato), possibly implanting them into him when he was a baby. This would go along nicely with how when Tobi was confronting Konan he said they were his eyes in the first place (at this time he was still presumably Madara).
3) Multiple Rinnegans
I have read in other posts how people thought that the way that the Rinnegan is shared (between the 6-paths of Pain/Jinchurikis) is by the black rods. My thought/take on this though is that they are separate Rinnegan (just as the sharingans are separate (my 'proof' behind this is simply how Tobi had a wall of them))
One would only naturally then ask how Tobi had obtained multiple Rinnegan. This then seg-ways into how the Rinnegan is formed. I do not remember if this was stated anywhere (manga/forums/ect) but here is my take on it.
It has now been stated that after the sharingan one obtains the rinnegan (yes Sharingan; it is never stated that you must awaken the Mangekyou or the EMS to progress to the Rinnegan http://read.mangashare.com/Naruto/ch...0/page015.html).
My quick quirp on this is simply that to awaken the Rinnengan one must simply posses the eyes of the Uchiha and the physical powers of the Senju/Hashirama, in Nagato's case he was a distant relative and therefore possessed them as does Naruto (and yes theoretically if Naruto was given an transplant for whatever reason he may then obtain the Rinnegan; lord help us all if Kishi actually did that). Here it is stated that Madara absorbed some of Hashirama's power http://read.mangashare.com/Naruto/ch...1/page012.html and on the next page he looks under his clothes, i only assume that its too see something that resembled Hashirama as such the case was with Danzou.
So going off of that is it not possible that Tobi simply obtained some of the Uzumaki clan (or even some other's possessing the physical powers of the So6P) and implanted them with Sharingan, waited until they awakened the Rinnegan, then killed/took eyes back? Possible he couldn't have gotten near Nagato because of Jiriya or forgot about him or whatever you wanna think up of or say.
5) Summoning Kyubi???
My understanding of the Summoning Jutsu was when one signed a contract with another life form (animals most of the time) and then were then able to summon them to their location right? http://www.mangareader.net/93-97-14/...hapter-92.html Simple enough. But then what about the contract that is needed to sign? I can't show proof that every single summoning needs a contract but to everything we've been shown about it it does. (http://www.mangareader.net/93-97-19/...hapter-92.html)
My question is why is Madara able to summon the Kyubi. As shown here http://mangastream.com/read/naruto/23677185/11 Madara is clearly able to summon the Kyubi in the traditional sense (Hand-seals, put hand on ground (unless you are mid-flight Gai), then *poof*)
My only thought to this is that at a very early time Madara did make a contract with the Kyubi and when he learned that Madara had evil intentions with him he resisted to go along with the plans, thus forcing Madara to use the sharingan on him. This is almost an "the Kyubi is actually a good guy instead of a raging beast" thought.
As i said earlier i do not feel like these are theories for i do have little evidence to back them up and they are just my own thoughts on what may be/ect. Of course debate is welcome as well as your own takes on the subjects. Let the flaming commence.