It has nothing to do with planning or deliberate choice or feng shui. For most of Japanese history, the major cities were in south-western Japan near the inland sea, but not on the east or west coast.

Major cities throughout Japanese history are Nara, Kyoto, and Osaka, and they're near the inland sea, pretty close to one another. The region is called Kansai. Tokyo is pretty far from there, and was a sleepy fishing village until the lord who controlled it, Tokygawa Ieyasu, made it his capital (then called Edo). That was about 1600. The area also had a major important capital for about 150 years in the 12th-14th centuries, called Kamakura. Chosen because that was the ancestral home of the guy who seized power. When he lost power, that area quickly became depopulated. One benefit of the Tokyo area (called the Kanto in Japanese) is that it's sometimes known as the "breadbasket" of the country. The plains of the Kanto region are very fruitful. Meanwhile, a lot of international contact was to be had in western Japan, meaning that Kyoto, which was the capital of Japan for most of the nation's history, got new traded items and information before any area on the eastern coast. It's probably no coincidence that Tokyo, with its great harbor, became not just the political capital of Japan, but the population capital, once trade with other countries became so important in the latter part of the 19th century. That is, it was already the political capital, for the reasons named above. But Tokyo, and its near neighbors, Yokohama and Chiba, became major business centers because of the trade they had with the US and Europe, much more so than western Japan did.