Clearly Madara is behind all of this, I think we can all agree. The connection the Mist village, the network of Zetsu in the area... it all points to Madara the only question is to what extent Obito himself becomes aware of this; you'd think that at this point, the Tobi we know would see clearly that Madara had a hand in Rin's death.
I could see the irrational and traumatized Obito infusing himself with Spiral Zetsu's strength/intelligence if he's given proper motivation; in the last two chapters, Spiral Zetsu has constantly tempted Obito with this possibility, and also stated that the Zetsu are more intelligent than human beings.
One interesting thing is that Obito saw through the eye he'd given Kakashi. This reminds me a bit of the Rinnegan's shared vision. Not sure how it's relevant, but perhaps it's another watered-down Sharingan version of a Rinnegan ability.
I wonder what set of circumstances forced Kakashi to kill Rin. I also wonder if we'll get an explanation of where Minato was during all this. I'm expecting at least two more weeks of flashbacks... next week we'll see Obito return to Madara, and perhaps after that we'll get his final transformation into Tobi (along with Madara's death?).