The native Indian power that could most likely spread and rule over the subcontinent after the Mughals were the Marathas. After the collapse of the Mughal Empire, the Marathas had conquered much of North and Central India and for a time the Mughal Emperor was a puppet in their hands.
The untimely death of Shivaji, the succession disputes between his grandsons, the weakness of his successors etc. were all factors against the Royal House. Still the ascent of strong Peshwas(Prime Ministers) and brilliant generals helped the Maratha power to grow. The not so cordial relationship between the Peshwas and the hereditary commanders like Bhosley, Scindia, Holkar, Gaikwad etc. prevented the consolidation of the Maratha confederacy. The defeat of the Maratha forces of Peshwa in the Third Battle of Panipat in 1761 at the hands of Ahmed Shah Abdali also was a great setback for the Marathas.
Shivaji expired in 1680 at the age of 53 and Aurangzeb died in 1707. If Shivaji had lived longer and consolidated the Maratha Empire, Marathas would have succeeded in replacing the Mughals as the dominant power, preventing the foreign incursions and interference.