I have had classes on Filipino history.

You must take into consideration that Filipino history is intentionally taught to instill nationalism in the Philippines. You can see this in Republic Act 1425 which mandates that students (including tertiary levels) in the Philippines have to learn about Rizal and his literary work.

You might see that a law which encourages the development of nationalism developed out of a perceived lack of nationalism.

Nationalism did not exist before colonial rule, and it is something that started to emerge as Spain spread its reach. The most important distinction between Latin America and the Philippines to understand is that very few Spaniards settled in the Philippines, and that they restricted themselves to a few cities like Manila (with the greatest Spanish presense), Cebu, Iloilo, etc. This is probably why Filipinos today do not speak Spanish.

You would have a great portion of Filipinos who experienced very little change from Spanish rule (with the exception of Christianity which was spread more widely). Then you have those who have been under more direct control of the Spanish.

The Spanish gave out parcels of land to be administered by their landsmen. They collected taxes in exchange for the development of their communities. It's at this point where you can see exploitation. Legislation was put into place which stipulated certain conditions which must be met before tax could legally be collected.

The situation for the Filipinos changed drastically in the early 19th century as the industrial revolution around Europe led to a similar agricultural revolution in the Philippines. Foreign countries started investing (they were taxed the same as Spanish businesses at that point) in the country, and cash crops (first tobacco, then Abaca or Manila Hemp, and then sugar cane) started to be cultivated.

A small, wealthy elite of Filipinos started to emerge because of it. The eventual revolution in 1896-98 was over Filipino participation in government (restricted to local governance), access to education, and land ownership (Filipinos were tenants of land).

To answer your questions directly:

Spain had immense problems managing the Philippines. The Philippines were attacked by the Chinese, Dutch, and British, all the while facing constant uprisings in Muslim Mindanao. There have also been localized rebellions which started to occur in the last century of Spanish rule but they were always restricted to their region.

Spanish rule defined the Philippines as a country for the first time, as such it was instrumental in creating a national identity, one that the Philippines today tries to actively counter. It did not however bring about a unifying national identity between Luzon and the Visayas, and Mindanao. Even today, parts of Mindanao are collected into what is called the Autonomous Region of Muslim Mindanao.