The premise of the question is incorrect. The East India Company did set up an outpost at Hirado, and the Portuguese at Dejima (Nagasaki) with the Dutch moving into both. In the early 17th century, the Portuguese were banned from Japan for trying to spread Christianity against the law of the Edo Bakufu, and the EIC closed down the Hirado post for being unprofitable. The Dutch remained at Dejima throughout the Edo period.

Germany took Qingdao in 1898, after China has just been decisively defeated in the First Sino-Japanese War, with China's main modernized forces destroyed by Japan in the process. So at that point in time Japan was a far larger military power in East Asia than China.

Greetings! This is certainly an interesting question which almost (but not quite) verges on the "what-if" of history where the European powers managed to secure a foothold in Japan. A minor nitpick (excuse the pedantics) here, but there were several attempts by the Europeans to set up the equivalent of what would later become the Chinese "treaty ports" in Japan. I'll get onto those efforts in the first part of my response, before then tackling the "why?" of their failure. Note however, that this by no means is an exhaustive writeup on the history of Western interactions with Japan pre-1853 (when Commodore Perry arrived with his infamous "Black Ships" and forced Japan to open itself to the world). With that preamble out of the way, let us begin.

During the years of the Tokugawa Shogunate (c. 1600-1868), the policy of the Japanese to foreign traders was simply summed up in one word: 'seclusion'. The shoguns of the Tokugawa era were particularly wary of efforts by European traders to "sell" their religions alongside their trade goods, fearing that such influence would lead to the rise of internal threats with support from the Europeans. Under the shogunate of Tokugawa Iemitsu (r. 1623 - 1651), the Spanish and Portugese traders were forced to leave Japan, barred from ever entering it again. In another edict, Iemitsu forbade all remaining foreigners (namely the Dutch) from travelling inland, as well as selling or giving books to any Japanese person. Thus by the 1640s, Europe's link to Japan had been all but severed. Only the Dutch remained to trade, but they were content to abide by the strict regulations imposed from Edo. All they had was a small trading outpost on the "landfill island" of Dejima, in Nagasaki harbour. Rather interestingly, the Dutch (mainly representatives and merchants of the Vereenigde Oostindische Compagnie, or United East Indies Company) were highly discouraged from even learning Japanese, in an effort to avoid them getting too "close" to the local populace whom they interacted with.

Interestingly enough, this isolation did not stop other European nations from trying to set up a colony-like holding somewhere on the Japanese islands. The British had attempted to mimic the Dutch, going so far as to set up a factory at Hirado in 1613, but this effort was abandoned just ten years later (in part due to the Dutch dominance of trade, and also due to the increasing reluctance of the English merchants to invest in the Far East trade). Thus from the 1640s up until the 1850s, Japan remained a closed country to the West; though not, and we must stress, not, an isolated country from the rest of Asia (but we digress from the main point there). Even as late as the late 1700s and early 1800s, the prevailing thought of bakufu (shogunate) officials and daimyo was that legitimate rule of a unified Japan meant the exclusion of Western nations from its affairs. Below is a revealing bit of writing from Tokugawa critic Aizawa Yasushi, which illustrates such a sentiment:

Recently the loathsome Western barbarians, unmindful of their base position as the lower extremities of the world, have been scurrying impudently across the Four Seas, trampling other nations underfoot. Now they are audacious enough to challenge our exalted position in the world. What manner of insolence is this?

From what we have described, there was also another problem with simply "blasting Japan open" to the Europeans: its government structure and warrior culture. Though the bakufu was certainly not as centralised per se to the equivalent governments in Europe, by this period of Japanese history the fractured clan-based civil wars and intrigue of the Sengoku Jidai era were no longer present. For any European power, maintaining a considerable "expeditionary force" if you will (not to mention the required naval assets for many) would be a wasteful and costly experience on the whole. Further, from the 1640s to the 1850s the many European powers were occupied elsewhere in Asia, the Americas, and even (though to a far lesser extent) Africa to place serious thought into "colonising" the Japanese mainland.

There were however, as mentioned earlier, attempts to curry favour with Kyoto. Russian fur trappers and traders, having reached the eastern shores of Siberia, attempted twice (once in 1792 at Hokkaido, and again in 1804 at Nagasaki) to ask the bakufu to grant them trade privileges. They accepted a polite Tokugawa refusal. The British then attempted again in 1808, when the HMS Phateon entered Nagasaki as part of the Napoleonic Wars (and caused quite a stir by capturing the Dutch trade representatives stationed there). The British returned again in 1818, sailing into Uraga bay near Edo (modern-day Tokyo). Again the offer to trade was turned down by the Tokugawa bakufu, and in 1825 the sporadic efforts by Europeans to set up further trade with Japan caused the bakufu to escalate the "isolation" policy: to expel by force any foreign vessels in Japanese waters. Under such measures, the American ship Morrison was dismissed by (harmless) cannon fire in 1837, and the Europeans heeded the warning to remain at a distance to Japan.

It was only in 1844 that the Dutch sent the bakufu an entreaty (request) written by King William II. Andrew Gordon on this unassuming letter:

They [the Dutch] explained that the world had changed: The Japanese could no longer remain safely disengaged from the commercial networks and diplomatic order that theWestern powers were spreading throughout the globe.

As further proof of this, the Japanese needed to look no further than their longstanding neighbour and rival: China. The First Opium War had just been concluded, in which a mere handful of "western barbarians" (in this case the British) had beaten the Celestial Empire, and forced the Qing government in Peking to submit to their demands for greater trade rights. Interestingly, as a result of the British gunboats demonstrating their superior firepower over Chinese coastal structures, the bakufu in Kyoto relaxed their own "shoot first; ask questions later" restrictions from 1825. When Commodore Perry landed in Edo bay in July 1853 with four "black ships", with a harsh warning to the Tokugawa government:

“The undersigned, as an evidence of his friendly intentions, has brought but four of the smaller [ships of war], designing, should it become necessary, to return to Yedo [sic] in the ensuing spring with a much larger force."

When Perry did return in 1854, and with nine ships to back up his words, the bakufu ceded their isolationist policies, and signed the Treaty of Kanagawa, which was later extended to include the European powers (Britain, France, Russia, and the Netherlands). The terms of this "Unequal Treaties regime" were similar to those that had been imposed on China just over a decade earlier, and even accorded European nationals exemption from Japanese law even if they were on Japanese soil. As Gordon writes:

"The treaties imposed a semicolonial status upon Japan. Politically and economically, Japan became legally subordinate to foreign governments. Over the next few decades, petty insults were heaped one upon the other. Numerous nasty crimes went lightly punished, if at all. In the 1870s and 1880s, these injustices—a rape unpunished or an assault excused—came to be front page material in the new national press. They were experienced each time as a renewed blow to pride, yet another violation of Japanese sovereignty."

But why then, did this not go any further? Why did no single Again we must return to the geopolitical reality of the world in the 1850s. The European powers were investing a considerable portion of their diplomatic power in China, where another Opium War (1858-1860) would force yet more concessions to the Europeans. Further, the Japanese had not been defeated militarily. Instead, the Unequal Treaties had been signed on the basis that Japan was not an equal member of international society; it was not a modern industrial, technological, cultural, and constitutional polity. It was this urge to end the Unequal Treaties which would drive much of the reform (and as some historians have termed it, "revolution") of the Meiji Restoration to come.

Part 1 of 2