After watching the Shippuden Ep. 55 and hearing the talk about yin and yang chakra, I got to thinking about how the two types relate to the kyuubi, the Sharingan, and Naruto's "that jutsu". I decided to start from the facts that we know first.
1) The kyuubi called the Uchiha clan (and the chakra of their Sharingan) cursed, even more sinister than his own chakra.
2) Minato separated the yin and yang chakra of the kyuubi upon the sealing into Naruto. The yin he left with his son, the yang was sealed away.
3) Madara and his bro were the first Uchiha's to unlock the MS. Thus it is reasonable to assume that before this event there was no relation between the Uchiha clan and the natural catastrophe known as the kyuubi.
My theory about yin and yang chakra is similar to that of the philosophy from which they spring. They are opposing, yet complementary "natures" of chakra which every shinobi possesses. Certain jutsu can be performed using them together with different amounts of each.
To a lesser extent, the yin and yang chakra also represent the good and evil that can be found within each shinobi as well. For the most part they tend to remain in a state of balance within the average person.
In relation to Madara:
The manga implied that Madara and his brother (or perhaps just Madara himself) killed or spilled blood to attain the MS. The breaking of bonds represented by that act changed one or both of them on a spiritual level. The yin and yang that was normally balanced within each individual shifted dramatically. They gained power and techniques but at the risk of their spiritual/physical health as a result of the imbalance. Thus, Madara began to go blind.
Yet it wasn't so with his brother. Somehow his brother had managed to maintain the balance within himself and within his eyes, so the transference of eyes from one to the other restored the balance within Madara to a degree. The reason I say that the regular MS is based off of "evil" chakra is because of what we've seen from it so far.
1) A ninjutsu from hell that burns for 7 days
2) A genjutsu that tortures one for 72 hours
3) A spirit of unknown origins. Who knows what Susano'o represents, or it's effect on the user?
For the most part these techniques have been dark natured, leading me to believe that they came about as a result of the imbalance created by the killing of one's best friend.
In relation to kyuubi:
A natural occurence said to occur whenever human malice has been allowed to foster. Or you could say where the evil side of people's spirits reigned. I believe that the kyuubi was a creature with a largely imbalanced chakra as well, largely leaning towards the yin. It was attracted to evil because it itself was evil. That is why I believe that Madara was able to master and control it. As evil as kyuubi was, Madara was even more evil. Thus his yang chakra overcame the fox's and he learned how to control it. Remember, that all possess both even if one is largely overshadowing the other.
What does this mean for Naruto? This means that Madara can't touch him. If the light side of the chakra has been sealed inside of him and the dark side is beyond Madara's reach then Madara effectively has his hands tied regarding the kyuubi. Minato knew this, and Madara knows this as well. Thus, the reason for Sasuke.
I think he needs Sasuke because of the potential that lies within his eyes. If Madara truly is a shell of his former self like Itachi implied then his eyes have weakened, possibly past the point of being able to control the fox. But Sasuke's haven't. His yang chakra was powerful enough to suppress the kyuubi within Naruto to some degree, without the MS to aid him. So I think that Madara will end up using Sasuke to go after Naruto. With someone who can suppress the kyuubi's yang chakra while still strong enough to hang with a normal Naruto, Naruto will have no choice but to draw on the yin chakra of the fox wherever it may be.
Thus, we come to Naruto's mystery jutsu. The most likely purpose for it is to fuse the two chakra within himself to grant it all of its power. His own chakra would theoretically suppress the evil inherent in fox, preventing is from affecting him adversely. If Madara can get Naruto to do this, then the kyuubi is within his grasp again through Sasuke. The AK was formed so that Madara would have a way of sealing the kyuubi for use without having to use his eyes since they'd grown weaker. If the fully formed kyuubi is sealed within the statue, Madara will not only have control over the fox but over all the bijuu in the world as well. Diabolical, is it not?
*I'm pretty sure I mixed up yin and yang in there more than once, so I'll just correct myself here and allow you to substitute accordingly.
If I'm wrong, please correct me.
More addendums to the theories are found on page 3, since this post isn't able to contain it all. You will find them under this same screenname, posted on 1/22/09 or sometime near that depending on where you live. Enjoy, and hit me with the feedback!