Because all the places Japan DID go to war with the US and European states over, were past the Philippines.

The economic isolationism brought upon Japan by their war in China, left Japan 2 options, stop the war or gain access to those raw materials themselves. The oil, rubber, rare minerals, and ore required to support a modern war machine. While there were some to be found in the Philippines to be sure, the real motherload was in the Southern Resource Area beyond, the Dutch East Indies, Borneo, the Malay peninsula, the region could keep Japan's economy running, if they could be seized and transported back to Japan.

However Japanese High Command saw no way they could do an end around and attack Britain and the Netherlands, and bypass the Philippines and not draw the US into the war too. While the US Asiatic Fleet was relatively small and toothless, and their was only some airpower it could not be ignored. So long as there were forward US based astride Japan's vital sea lanes to their planned conquests the life blood of the Empire was in danger. While the US had long since abandoned any ideas of rushing to the islands' defense under War Plan ORANGE, that did not preclude small support, or attacks elsewhere in support, while Japan would need time to finish seizing islands and reinforcing them with units freed from taking the DEI to serve as the first line of defense. Mutually supporting islands to bleed a relieving force or advance dry would take time to set up, and there simply were not enough units, or resources to do that while still at peace or not use those future garrison units in the initial conquests, or more units would need to be diverted from China.

So in short if war with the US could not be avoided in seizing needed resources, and Japanese leadership thought it couldn't, then the Philippines were in too important a position to ignore. While there were not sufficient forces to accomplish all tasks at once, and maintain a force to keep US forces in the Philippines in check too.

The attack on Pearl Harbor was Yamamoto's gamble to change the equation by allowing the IJN a period of relative freedom to maneuver and be able to stick to a relatively strict timetable.

The main reason is that the Philippines lie between Japan and the oil, rubber and other strategic resources of Southeast Asia, and the Philippines were a U.S. possession in 1941. Japan couldn't move to seize colonial possessions in Borneo and Indonesia while leaving a fortified American base straddling their lines of communication, and the initial invasion of the Philippines was timed to coincide with the Pearl Harbor attack, as well as attacks on other US and allied bases in Southeast Asia. The goal was to establish Japanese control over not only the Philippines, but to push a defensive perimeter out to the Malay Barrier and eastwards towards the U.S.

I got into this more in this older comment, but in the prewar period Japan's doctrine was create that defensive barrier, attrit the U.S. fleet as it steamed to the defense of the Philippines, and defeat it in a decisive battle somewhere near the Japanese home islands. The idea was that doing that would compel the U.S. to sue for peace -- it worked in the Russo-Japanese war, after all. If anything, the attack on Pearl Harbor was added to Japanese war plans fairly late in the game, after the success of the British attack on Taranto.

As to "why not focus on Midway," that was a bridge too far for Japan to contemplate, given its shipping limitations. The eventual attack on Midway was less about the invasion of the atoll than it was about attempting to draw a US fleet out from Pearl where it could be defeated.

Oh thank you. This makes much more sense now.