In general, Indian nations that are using the generic North/South Indian mission tree would benefit from their mission tree getting a similar treatment to the upcoming Malay nations' mission trees. While all Malay nations have an extensive mission tree with 15 shared missions, the remaining two branches are devoted to missions unique to each nation, giving Malacca, Champa, Aceh, Brunei, Sunda, Tidore/Ternate & Bali different things to strive for, even if the majority of their mission-tree is the same for all of them.
Another way to make India more interesting would be to add formable countries to the region, thus giving some of the minor nations more interesting things to strive for. Unfortunately, I have no idea which tags would be suitable for being suitable as formable or reformable, since I'm not really well-versed in Indian history.
Wouldn't it then make sense to give Jaunpur a short mission-tree that encourages them to form Delhi, as well as missions and events that depict the hardships that fell upon Nagaur and historically led to the country's annexation?
Agreed. Deccan Sultanates and Vijayanagar successor-states don't appear in the game enough, and having the blobs in Southern India actually able to collapse would help to make the region more dynamic.