I think that one of the most challenging elements to Indian history would have to be its birth in the modern setting.  The idea of Partition is still something that is not entirely clear.  Partition is a controversial topic because of how it was conceived, its impact on India then, and the issues that face the nation today as a result of Partition.  The idea of arbitrarily dividing a subcontinent where Hindus and Muslims, as all as Sikhs and Parsis lived so close to one another into nations of "majorities" was problematic.  Consider the Partition Riots and the slaughter as well as displacement of millions as a result of this.  Partition is a controversial topic in Indian history because it cannot be considered an easy success.  It is one in which for every narrative where one can defend it, an alternative narrative about its destructive nature can be found.  The idea of Indian politicians sitting with British leaders and drawing absolute lines that would determine the lives of millions without full acknowledgement of the cause would be a reason why it is so controversial.  At the same time, the current dilemma faced in the Jammu- Kashmir provinces can be rooted to Partition.  In not being able to fully speak for this part of India, recognizing where it might choose to be, the Jammu- Kashmir issue dogs India even today.  It is one in which the overall issue of Partition's success has to be assessed and debated.  It is here where I think that one can see that Partition would be a controversial issue in Indian History.