Allow me to stress my view on "the real Uchiha prodigy."
And as much as I dislike him, all the hints are pointing to Sasuke as the true successor of all doujutsu wielders.
From what we have seen so far the true prodigy of the Uchiha is Sasuke.
Whether due to DNA reasons or not Sasuke is extremely intelligent. Sasuke's learning curves are similar to Minato, in regards to him only having to see it a technique once and he understands the properties of it, and how it can be further advance and much more. He is a gifted tactician, as he will actually use the above to help him understands his opponents strengths and weaknesses, which allows him to win numerous battles that otherwise he should lose. And this is not even including his incredibly high charka levels and reserves.
Madara is the only Uchiha aside from Sasuke to have a ridiculously high charka levels and resides compared to other Uchiha. What this ultimately means is that he can spam a number of devastating doujutsu techniques before getting fatigued. However the huge thing that separates Madara and Sasuke is potential, is Sasuke's potential.
Sasuke's charka in particular is much more potent then Madara, which conclusively means, that Sasuke's potential is far greater than Madara's. Sasuke has the potential to become the strongest doujutsu wielder (apart from the Sage) that their ever was. He has the promise to rival the Elder Son in terms of overall power, but the intelligent to surpass the Elder Son and become something greater.
The greatest hint of all, is why does Tobi want to "stimulate" Sasuke with Naruto, when he has a plan that is supposed "to end it all?"