The difference in pattern adds a little more credibility to the idea that the Elder Son's eyes may have been closer to that of the EMS than the Rinnegan. The pattern of the Elder Son's eyes also remind me of Tobi's swirl mask. I am still suspicious that their are two aspects of the Mangekyou sharingan, as we have seen, Kakashi and Tobi both have eye powers that seem to manipulate space. Powers that seem quite different from the ones that Itachi, Sasuke, and Madara have shown. We still don't know enough to confirm why different Mangekyou seem to have different abilities but some are the same. Perhaps this is due to the impurity of the bloodline. Perhaps the Elder Son had all of the Mangekyou abilities that would be another possible explanation for why Tobi needs Sasuke. Perhaps Madara's EMS was incomplete, Sasuke still has a chance to awaken the true Eyes of the Elder brother which are also needed to create the true Rinnegan.
We know that Madara was attempting to recreate the bloodline of the Sage of Six Path's within himself but we also know that he failed for some reason. Sasuke seems to be key in his plan of recreating that power but so far we haven't really seen any indication that Sasuke possesses something that Madara lacked. So perhaps it is that Madara made a mistake and tried to complete the Rinnegan without all of the necessary parts, as a result his Rinnegan was incomplete and so he attempted to evolve it further by giving it to another descendant of the line to develop it further. This could explain why the Rinnegan was given to Nagato. Now the eyes have absorbed Nagato's bloodline and been developed more but they still only represent one half of the who, which would explain why Nagato's rinnegan didn't possess any powers that the sharingan has. Madara himself is able to use Susanoo with his Rinnegan because he was an Uchiha who had already mastered the Mangekyou Sharingan.
Tobi is now using Sasuke to completely master the Elder Brother's powers. Tobi has since obtained and mastered some of the powers that Madara himself did not have at the time of his death. The time/space abilities. As I said in a previous post, I think the fact that we still haven't been told how Kakashi obtained his Mangekyou Sharingan is very significant. I think there are other conditions to awakening a different set of Mangekyou powers. It is possible that Tobi understands the process of combining these powers but he needs Sasuke (the last pure blooded living Uchiha) to recreate the true power of the Elder Brother's eyes, then by combining those Eyes with the Rinnegan he already possesses, he will create the true Rinnegan, the one that only the Original Sage of Six Path's possessed.
What I believe Tobi and Madara fail to understand though is that obtaining the power of the Sage Through scientific manipulation will not grant them the power of nature that is truly needed to control those powers the way the Original Sage was able to because he did it by mastering natural energy. As a result I think that when Tobi/Madara becomes the Jinnchuuriki of the Juubi he will lose control and the Juubi will break free. Naruto, who will have mastered the Sage Arts by that point and learned to balance Bijuu chakra with Natural energy will be the only one capable of being the Juubi's Jinchuuriki.