Why bother with the Phillipines at all, and not turn north to get closer to Japan. ...
This is quite true. Taking the Phillipines will definitely cut off the head of the snake, severing it from the oil of the DEI. However, I might be able to interdict from the Marianas if the air garrison in Luzon isn't crazy. Another factor is the major shipyard in Manila as well as the large number of victory points available from its capture.
The question is whether one should let oneself be guided by the arbitrary distribution of victory points. If the scenario designer had set but a single victory point on Tokyo, would that influence your decision?
By starting a scenario that gives the Japanese an ahistorical industrial capacity you have already tilted the balance a bit against a strategy of attrition (since attrition will be harder to achieve than it historically was).
The Philippines are not the head of the snake, they are its spiked tail. The head is the island of Honshu. Given the choice between a war of attrition and the option of a decapitation strike, I in the finest traditions of German warfare must recommend the attempt to decapitate. It may not yield as many victory points, but they are just window dressing.
Of course, I don't know enough of the inner mechanics of WitP. If the Phillippines' production capacity is so large that it allows Imperial Japan to build up a fleet of epic proportions that could seriously threaten your supply if you, say, had captured Okinawa and were preparing the invasion of Japan, then it may be necessary to take the PIs first. But I would do so only if they have the potential to become a bigger problem than the Japanese islands themselves.