Original time line Indonesia alone has a tremendous amount of diverse ethnic, lingual, and to some extent religious groups. True, there are some obvious dominating factors, with a Javanese population which forms the centerpiece, and a majority Islamic population, but Indonesia shows that diverse political groupings on such a size and scale can exist. Indonesian nationalism comes from the legacy of Dutch rule in the region, and the resistance to it. Benedict Anderson devotes an outsized amount of his Imagined Communities to Indonesia, and a key point is that former Dutch administration and rule meant a creole nationalism could develop, one that proved to be incredibly strong in the end. India and Indonesia despite their diversity and vast populations, are workable political concepts.
By far the easiest way to have it work is to have it fall under a single European entity which administrates them as one block, and supports keeping them together at independence. The Dutch or the English are the two versions of this. I would think that the Dutch would be more likely to do so than the English, as the English, like originally happened with Singapore and Malaysia, will probably separate it out. But regardless, as long as one does get these factors to happen, then there will be a nationalism that will exist, that'll imagine this greater Indonesia into creation.
Developing a Greater Indonesia by the independent states is extremely difficult. East Timor was, and is, a small, poorly populated, and economically backwards state, but Indonesia proved incapable of holding onto it in the long term. For Malaysia and Singapore, the difficulties would be tremendously magnified. Once a nationalist imagination is set into place to compete, things get much harder. But the formation of nations and nationalisms is tremendously fluid when being created, and could easily accomodate such a Greater Indonesia concept if caught early enough.