Sorry, I meant my previous post to be sarcastic. I should have indicated that better.
Obviously these concepts are mostly distinct. Nothing is cut an dried, but I still think that Indonesia is an inappropriate choice. To broaden it from individual empires to cultures I would say use the Javanese (which includes Majapahit, Kediri, Singhasari, etc.), or the Malay (Srivijaya, Sultanate of Malacca, etc.).
Yes India is in the game, but "India" as a name dates back to the ancient Greeks. It would be neat to have distinct north and south Indian civs, but while you could use say the Tamil for a southern civ or even widen it to the Dravidian, what would you call the northern one? The Magadhan? It was the center of power for the north during most of the pre-Islamic period. That's why "Indian" works. It's an historical term and it encompasses the whole of the diverse sub-continental civilization. The Indian civ in the game is a wide one similar to the Polynesian, Greek, Celtic, or even German.