The Philippines does have a few cities that are filled with Colonial-era buildings such as Zamboanga City.
Manila has the Intramuros area that is dominated by Colonial-era buildings. Even McDonalds is in a Colonial-era building.
The main reason why cities like Manilla lack as many of them as say, Hanoi, is World War II. The Philippines was probably the third most impacted country in Asia by the Pacific Theatre, only after China and Japan. No other country in Southeast Asia was hit as hard.
This is what Manilla looked like in 1945:
Here is what Manilla looked like in the 1930s:
When US troops approached Manilla, Japanese Rear Admiral Sanji Iwabuchi ignored an order to retreat, saying that he was “too ashamed” to obey that lawfully-given order, and led 19,000 Japanese troops in a month long massacre of between 100,000 and 500,000 civilians and an eventual mass suicide as the US advanced into the city.
In a controversial court case, Sanji Iwabuchi’s superiors, Tomoyuki Yamashita and Akira Mutō were tried and executed for war crimes even though they ordered Admiral Iwabuchi to retreat and he defied their orders. Numerous American Army JAG lawyers were upset by this because neither men offered to defend themselves, their lawyers did not provide very good defences, and both essentially just allowed the courts to find them guilty.
No other country near Southeast Asia experienced anything close to that except for Burma and Bangladesh. They suffered most of their casualties through mass starvation in one of the worst famines in human history (which, historians still debate on today as to exactly how culpable Winston Churchill or the Japanese were and whether or not it was intentional; see Bengal famine of 1943).
Most of Southeast Asia was skipped over. Japanese troops were still in Indonesia and Malaysia when Japan surrendered in 1945 because the US and ANZAC essentially skipped over most of them, island-hopping from Papua New Guinea and Guam to the Philippines, then the Philippines to Okinawa, and then eventually Okinawa to Japan (although the last leg never eventuated into a ground war).