MacArthur's real failures were in not defending the Philippines. Other than this the Pacific campaign was fine in my opinion. Granted I have criticized MacArthur for wanting to invade the Philippines and Indonesia in 1944 instead of Taiwan. I don't think that this was really a game changing decision.
Part of me thinks that there is no point in attacking Philippines and Indonesia since the Japanese didn't seem to be capable of sending convoys of resources back to Japan and could easily be intercepted by the USN, especially if they had just taken Taiwan and cut off the Japanese.
On the other hand I kind of get the feeling that the decision to invade the Philippines and Indonesia was calculated not only to give the Army time to prepare for Operation Downfall but also to give a psychological shock to the Japanese. Taking Taiwan would be helpful in the Pacific but the Army never intended to engage the Japanese on mainland China, especially when they could just attack Japan directly. Neither Chiang nor Mao showed any indications that they would roll up the IJA on the mainland either. So I'm not sure that taking Taiwan would be very helpful to the Chinese, but it is often part of the Formosa argument. When in fact FDR had largely shifted his policy with regards to China, recalling Stilwell, believing that USA could come to an agreement with Mao and generally just giving Chiang equipment. Chiang was not willing to fight by FDR's rules and he was not willing to carry out massive and costly offensives to retake China, when he could just wait for the USN to blockade Japan.
Actually I think that MacArthur gets way too much criticism, especially later on for Korea. When not enough criticism is directed towards the civilian authorities. Truman probably was as impotent as they claim.
All of these questions are worth investigating. Crucial to the argument would be what sort of preparations the Japanese made to defend Taiwan. For all I know the Americans would be in for another Okinawa and Iwo Jima type of scenario. So the Philippines and a few areas of Indonesia probably were much easier targets at least operationally and in terms of IJA troop deployments and dispersals. Also it isn't like the USN didn't want to wipe out what remained of the USN which was largely concentrated around the Philippines.