The grievances of the Filipinos with regard to Spanish rule were very similar to the grievances expressed by others who rebelled against the Spanish. In the Philippines, as in places like Mexico, the rebellion against Spain was mainly led by local elites who were unhappy about being treated as second-class citizens. They typically wanted reforms rather than independence.
The Filipinos who led the rebellion (like Emilio Aguinaldo) were the ilustrado elites of society. Most of them were not ethnically Filipino (at least not full-blooded) but were various types of mestizos, often with Spanish and Chinese blood. These were the richest and best educated.
The ilustrados had been educated in Enlightenment ideas. They felt that the government should govern more for the benefit of the people. They felt that all people of talent should be allowed to rise as high as they could rather than experiencing discrimination based on race or ethnicity. These were the cores of their grievances. They wanted equal opportunities for all and representation in the Spanish legislature. They wanted political freedoms. They also wanted tangible signs of enlightened rule. They wanted more and better schools. They wanted honest bureaucrats and judges so they would not be ruled by corrupt and partial officials.
At the lower levels of society, the grievances were less philosophical and more rooted in everyday life. The peasants simply wanted better treatment. They were tired of being treated brutally by corrupt Spanish officials and tyrannical Spanish priests. Their anger helped bring many of them to side with the ilustrados.