Recall from the Manga the meeting between the 4th, Kisame, and Madara/Pseudo-Madara. In the manga this is what the page looks like,

http://www.narutobase.net/manga/Naruto/507/13

In the middle bottom panel it is clearly shown that Madara/Pseudo-Madara has bandages on both of his legs. I know that the anime likes to add stuff that isn't shown in the manga, but I couldn't help noticing this image:



In this image is can be seen that Madara/Pseudo-Madara right arm has bandages on it and his left does not. This seems like too much of a coincidence to me. I think this coupled with long haired Obito in the last chapters is pretty concrete evidence that he was controlling the 4th.