Really only few Mughal rulers are hated, majority of the rulers are actually loved by the populace. Let me recount them.
Babur (He is seen as an Turkic invader from the Steppes, he was kind of ousted from his afghan-timurid homeland and was finding a new home to establish his dynasty, he is one of those disliked rulers)
Humayun (He didn’t really have a long reign, he was just trying to defend the land his father had newly conquered)
Akbar (He is one of the most beloved Indian Rulers, he is known for putting the foundation for the powerful tolerant Mughal Empire. He united north india through diplomacy and tactics. He extended a Rajput marital relationship and heritage for the Mughals. Thankfully he is the leader representing Indians in the game, he truly is Akbar the Great)
Jahangir (He had a peaceful, loving relationship with Rajputs just like his father)
Shah Jahan (He brought the golden era of Mughals building many Magnificent Monuments. He is known for his amazing architectural renovations)
Aurangzeb (he was the tyrant who finally ruined the reputation of mughals once and for all, he killed all his brothers and jailed his own father to take over power, he massacred hindu population intentionally imposing harse anti-non-islam tax such as zaziya, he is fought wars with deccans chattisgarh-orissa and forcefully annexed them but in turn he finished emptied the treasury of mughals and now farmers and non-muslims revolted all over the empire. sikh and maratha took the oppurtunity to declare independance from his tyrrany, he is the most hated mughal ruler)
Many small mughal rulers came inbetween but nobody is really significant since the dynasty was in ruins.
Indian populace remembered the mughal rule and revolted the british with Bahadur Shah Jafar (last Mughal ruler) as their figurehead. Since mughals were the unifying tolerant empire they could look upto instead of the company who was just trying to exploit and loot the wealth out into england.
India is a land of many diversities, really one civilization doesn’t do the justification for it. We need more than one to represent all the different cultures and kingdoms. Mughals in the early modern era are the only option that represent the Indians as one civilization.
Aurangzeb is the offensive ruler who created the hindu-muslim hatred which further broadened during the colonial era when British promoted things like separate hindu-muslim cricket team, separate political party, separate reservation, divide-and-rule etc. India is a huge sub continent and there are large number of cultures and kingdoms just like in Europe. Mughals are like the Romans. They were tolerant and that’s why they could give the unite the subcontinent and that’s why they were chosen as the unifyig figurehead in sepoy rebellion… Instead of calling for removing them due to some modern political hatred. We should be calling for correcting/adding more historical elements to the game.