It's worse than that because Japan never intended for any of the "liberated" countries to have self-determination. When Japan said "Asia for the Asians" they really meant "Japan should rule Asia." Manchukuo may have been "independent" on paper, but everything was actually decided by Japanese "advisors". Expect the same thing for any of the "liberated" countries in Asia.
While there will always be collaborators of some sort, the independence movements of those countries will all quickly turn against Japan as it attempts to control those countries. It won't just be the Philippines. Nehru, Ho Chi Minh, Sukarno, etc. will keep agitating for real independence. They won't settle for being puppets.
Japan has less economic power than Britain and France did at their height, so they would be very pressed to maintain control in their new empire. China alone was a huge drain on the Japanese economy. How are they going to hold onto India?
Japan would have various options to hold together the "Greater East Asia Co-Prosperity Sphere", but it is going to be a ramshackle effort. At best, it will likely lose any real power over India very quickly, and be sucked into low intensity warfare over most of East Asia. It would continue to be the paramount power in Asia, but likely faces real threats in other Pacific/Asian powers like the US, Soviet Union, or a Nazi dominated Europe (which likely exists since the only way Japan could win is if the Nazis somehow win).