Under Akbar, the Mughal empire had nothing worth mentioning south of the Vindhyas. And in the north, Kangra and the hill states were all free. Kashmir was conquered only in the middle of Akbar's reign. Akbar presided only over the Indo-Gangetic plain. The Rajputs of Mewar and Malwa were fully independent - Malwa was supposedly conquered, but the Rajputs kept rising in revolt there too.
Under Shah Jahan, the Mughal empire already encompassed Berar and Ahmednagar, and towards the latter part of his reign, also Bijapur and Golconda. Except, as the empire grew, so did the instability. Basically, by the time Shah Jehan pacified one region, another would rise in revolt. Nothing south of the Vindhyas was stable, and more importantly, even the heartland was becoming unstable. His stupid attempts to conquer Kandahar by force did not help either.
Most of Aurangzeb's problems were inherited from his father's time. He exacerbated the problems, but he did not create them. His father had already broken the power of Ahmednagar and Berar, and weakened Bijapur and Golconda. In their place, the new power of the Marathas rose in the vacuum. It was a failure of the Mughal empire to control anything south of the Vindhyas effectively that was the problem.
The Sikhs had already risen in revolt during Aurangzeb's reign itself. The Bundelas, the Jats, the Ahoms, and the Rajputs had done the same, not to mention the trouble with the Marathas. Basically, by Aurangzeb's time, it was game over for the Mughals. It was just a question of how long the agony could be prolonged. As long as the Mughal empire confined itself to the Indo-Gangetic plain, it was reasonably secure. Once it tried to expand beyond, it became unstable.