I've delved into this question a few times in the past. Feel free to review them here and here.

However, to summarise the points made in those posts: it is difficult to analyse Japanese policy in the late 1930s and early 1940s on a whole because, in many ways, there was no consistent Japanese policy. Japanese decision makers were, in many ways, desperately trying to react to a rapidly unfolding situation while also attempting to manage very strong domestic pressures. The most important of these--by far--was the ever expanding "China Incident". Ultimately, everything comes back to the war Japan is fighting in China, and the Japanese attempting to bring that war to an end. By 1941, in many ways, the war in China had placed Japan in a no-win situation. The ever expanding scope of the conflict had dragged most of the Army into a never ending war in rural China, while also souring relations with the United States. Japanese leadership was trying to find a way out of the China War, however, the preeminence of the armed forces; the sheer cost of the war in China in terms of blood and treasure; and the sense that Japan had been repeatedly "snubbed" out of the fruits of its victories in the past made it so that the Army (and the wider population) demanded large scale concessions be made by China to Japan. Such concessions were absolutely unacceptable to the United States, which began to increase the economic pressure it placed on Japan in an attempt to bring the Japanese to the negotiating table. However, if Japan gave in to US pressure, there would be substantial backlash among both the military and civilian populations, that would almost certainly lead to the collapse of the government at best, and an Army coup at worst.

This left Japanese leadership with very few palatable options. On one hand, simply continuing the war in China in spite of American pressure was unsustainable. The American embargo on oil and especially the embargo on scrap metal threatened to rapidly erode Japan's ability to wage war, all while American military strength expanded rapidly through the building authorised in the Two Ocean Navy Act. At the same time, conceding to American demands was politically unacceptable. This left the option of seizing the necessary resources from the European colonial holdings in the south. Importantly, in the minds of Japanese leadership, they were in a very strong "use it or lose it" situation, where if they did not use what military force they had now, they would be unable to use it in the future. Which, in many ways, is the meat of your question: why not attack only those, and ignore the US completely?

There were several factors that balanced against this. First and foremost was the Philippines. The supply lines from the Dutch East Indies and Malaya passed through and around the Philippine Islands, which at the time were an American colony, hosting American naval and air forces. Leaving the Philippines unoccupied meant that the US could very quickly strangle the supply lines from southeast Asia that Japan's industrial base would be incredibly dependent on. Secondly, the Japanese could not be certain that the US would remain neutral. The US had steadily increased the pressure on Japan throughout the extent of the war in China, and was providing loans and other military aid to China. It was entirely plausible that more aggressive action involving military forced could be the next step, and--if the Philippines remained in American hands--such action could be devastating to Japan.

Finally, and what is likely the most important, in many ways many in Japanese leadership believed war with the United States was inevitable. The Imperial Japanese Navy in particular had dedicated its entire existence to defeating the US Navy in battle, and--in some circles--there was a belief that a war between the Japanese and the West (represented by the United States) was inevitable, as the two races would have to clash in order to determine the future of Asia and the Pacific. Moreover, much as the embargo presented a "use it or lose it" situation to Japanese leadership, Japanese naval leadership saw the Two Ocean Navy Act passed in 1940 as a similar situation. With the massive increase in American naval power now authorized, even if the Navy's plans for whittling down the American fleet as it advanced across the Pacific played out perfectly, the survivors would likely still be enough to outnumber the IJN overwhelmingly. Thus, Japanese leadership saw a situation wherein: a) the US intervention was possible; b) US intervention with the Philippines as a base would be devastating; and c) the balance of naval power in the Pacific was shifting rapidly in favor of the US, to an extent Japan could not counter, d) there was probably going to be a war with the United States in the future anyway.

Given all of that, the Japanese decision was to strike while they still possessed enough naval power to maybe defeat the US Navy and maybe inflict enough damage on the US that the Americans would opt for a negotiated settlement, before the massive naval construction program brought too much power to bear. Just as a note, the Pearl Harbor attack was not intended to be the decisive knock out blow that would bring the US to the negotiating table. Rather, it was a massive flank guarding move, intended to delay the sortie of the US fleet, giving the Japanese enough time to take their objectives in southeast Asia, and build up their defenses in the Central Pacific to await the coming US counter offensive.

Hope this helps to answer your question, and please feel free to ask any follow ups. I'll try to get to them.

Sources

• Edward J. Drea, Japan’s Imperial Army: Its Rise and Fall (2009).

• David C. Evans & Mark R. Peattie, Kaigun: Strategy, Tactics, and Technology in the Imperial Japanese Navy, 1887-1941 (1997).

• Stuart D. Goldman, Nomonhan, 1939: The Red Army's Victory That Shaped World War II (2013)

• Eri Hotta, Japan 1941: Countdown to Infamy (2013).

• Mark R. Peattie, Sunburst: The Rise of Japanese Naval Air Power, 1909-1941 (2001).