Even without MacArthur, taking the Philippines made strategic sense.
You are either playing the short game or long game. In a short game, you want to go directly to Tokyo Bay. But is the US navy capable of wiping the Japanese Navy plus their land support in 1944?
For the long game, you strangled Japan, meaning route to oil, which is the Philippines. That is why in OTL the Japanese already committed their Battleships in Leyte and Surigao Strait rather than waiting for the US to go to Tokyo Bay before they commit their remaining Carriers and Battleships.
In political terms, It would have been dicey. The Japanese by end of the war would have handed their weapons to the Filipinos instead of the USA. There was no need to hand Philippines independence when the Japanese already let them declare it in 1943 and the Japanese were letting the Filipinos run their own Republic. US loses all its OTL influence to the Philippines, meaning no more basing rights.
For the Philippines politically, the 2nd republic would have continued rather than transfer to the 3rd Republic.