Indonesia + Malaysia = Greater Indonesia. Culturally it makes much sense to have Indonesia and Malaysian territories united under a single state. Geopolitical factors however, kinda prevented it from happening.
Was the Japanese occupation realistically sustainable, there was actually a plan by Japan to make a client state out of Malaysia and most of Indonesia.
The only chance, and a very remote and stretchy one at that, would be Maphilindo plan. I personally don't know how, but the last time I heard anything about Maphilindo, somebody said something basically this : either you would need to make early Indonesia much less lefty and turbulent, or prevent Malaysia from forming by having Indonesia and Phillipinese successfully tackle it. Then again, it may won't include Northern Kalimantan especially for the later case, at least not immediately, but you would have Indonesia, Malaya and Phillipines joined together under a custom union.
The source