One of the issues that comes with governing w In the region is the cultural plurality, especially in language. Indonesia has hundreds of different native languages, Javanese being a major one. By this point, Malay had already beed used as a unifying language, especially trade, religion, and politics. The VOC also used it for many of their administrative tasks. When decolonizing, they had a few options. They rejected Dutch as few actually used it in Indonesia (the Dutch never really attempted to force the language on the colony) and it was a colonial language. Javanese was a tempting option, as it was the most common native language. The problem was that it wasnt a language everyone spoke and a language which symbolized Javanese dominance over non-Japanese Indonesians. Malay, on the other hand, was the second most common language, being used as a second language among a high proportion of Indonesians. The inability for Javanese to unite a country that only half speak Javanese is pretty clear. Malay was a language that they had historically interacted with and had quite a bit of experience with. It also meant that attempts at regional unity would have greater chances, especially with Malaysia (though these attempts turned sour pretty quickly).

Basically it boiled down to history, unity, and practicality.

Let me know if you have questions or need clarification!