The British ruled Java during the Napoleonic wars, plus parts of Sumatera. Present day Indonesia only came under Ducth rule around 1920, 1912 if you don't include Papua. The major motivation for control of the East Indies is the loss of Belgium, after the Napoleonic Wars. The boundaries of British and Dutch spheres of influence in the Indies are laid down in the Anglo-Dutch treaty of 1824, before that the islands were free-for-all.
Indonesian nationalism is a unique thing. It started in the 1928 Indonesian Youth Congress, where it replaced Javanese, Sumatran, etc. nationalism, which were also unique as they island, and not race based. This lead to an educated elite advocating an independent Indonesia. Japanese occupation, in turn, turned these people into leaders, they used Japanese propaganda to spread the idea of nationalism to even the most illiterate peasants, while in turn the Japanese used these to send the people into forced labor. Some Japanese are truly sympathetic, however. One of them is Rear Admiral Tadashi Maeda, who funded Soekarno and Hatta's political trip all around Indonesia.
One place to start is the BPUPKI meetings during the final stages of WW2, BPUPKI was a committee set up by the Japanese, with a Japanese leader, tasked on planning Indonesian independence under Japan. Mohammad Yamin, lawyer slash poet, proposed that Malaya, Northern Borneo, and East Timor are also to be part of Indonesia. Support for it was limited however. If there were support for it, then maybe Indonesians would try to incorporate Malaysia.
We can also make Malaysia a less desireable nation for Malays. Prevent the ketuanan Melayu for example, and make the British ignore the Malay protests on immigration laws. The Chinese would start taking their jobs in the civil service. Perhaps then, support for a union with Indonesia might take off.