Board Thread:Naruto Discussions/@comment-945885-20140709082448/@comment-1512913-20140712204018

I'm certain that two different chakras merge over time when exposed to each other. Orochimaru hinted on this during chunin exams in the forest with a claim that it had been many years since Naruto became a jinchuuriki and that his and Kurama's chakra will eventually merge.

In the same light, the most likely reason for why it took years for Madaara to get the Rinnegan was because his Indra chakra needed time to merge with Ashura chakra into one.