Finally, a question close to heart!

Well, one specific reason as to why the Catholic faith itself was very successful in the Philippines is that it was a Spanish colony; Since 1565, and more strongly 1600s onwards, there had been a lot of institutions that sprung up n the Philippines that had the primary goal of spreading Christianity; The Dominicans, for example, established the Pontifical and Royal University of Santo Tomas in 1611, and still remains one of the bastions of Catholic education until today.

With the Jesuits, they had a rough and late start to be true, with establishing their primary base of Jesuit education at the Ateneo Municipal de Manila (now known as Ateneo de Manila University) in 1859 through the graces of Queen Isabella II of Spain herself, but it is through this institution that the Jesuits made their mark on the Philippines, since not only did the national hero Jose Rizal study in that institution but also the Jesuit teachings of empowerment and self-criticism proved popular with the Filipino intelligentsia (known then as Illustrados )

Now, with regards to China and Japan, the Jesuits failed not only due to their lack of base support from a rather powerful institution (in the Philippines' case, the Spanish Crown), but also because of local factors. Specific to the case of China, Pope Clement XI's decree in the Papal Bull Cum Dues Optimus aggravated the Chinese Rites controversy, which essentially condemned the Jesuit syncretization of local Confucian beliefs with Christianity with the method of using words like "Tianzhu" (which is Chinese words for heaven with Confucian characteristics), but that's a story for another time.

Essentially, with that Papal Bull essentially forcing down the Roman Catholic conventions of Christianity down the Chinese Emperor's throat, the Kangxi Emperor exiled all Christian missionaries from China, which led to the slowdown of missionary work in the Middle Kingdom.

Meanwhile, in Japan's case, the Christians posed enough of a threat to the delicate balance that the Bakufu wanted to keep that they were brutally repressed, culminating in the Sakoku policy which essentially not only closed off any Christian missionary work in Japan but also outlawed the religion entirely.

For sources on the limited success of the Jesuits in China, I recommend George Minamiki's "The Chinese rites controversy: from its beginning to modern times" which also contains a chapter on the side of the Jesuits' limited success in Japan, but for a more specific work on that, try "Handbook of Christianity in Japan" by Mark Mullin and Brill Leiden.

As for the Jesuits' success story in the Philippines, I recommend Horacio de la Costa's "The Jesuits in the Philippines", though it is a piece written from a Jesuit perspective.

I hope this helps!