Well, for the Philippines with regards to ATL, you need to take away OTL bias. Majority of the 19th century rebellions were led by Creoles or Pure spanish blood while the Indios were reluctant to even lead until 1890s.
1896-7, is mostly an Indio rebellion while the creoles and the insulares were a bit reluctant.
An example would be: Had this succeeded http://en.wikipedia.org/wiki/Andrés_Novales
Philippines would be independent around the same time as Mexico led by a dictator like Mexico's Santa Ana. So it totally depends on how you want to butterfly Philippines away or retain as its OTL form.
Hmm... I've actually been thinking of a shrunk Philippines lately; with Sulu and Maguindano under foreign protection and Palawan ceded to a different colonial power in exchange for independence ala. Bakumatsu Japan.
I might need to do a PM once the week is over.
The difference is that Sarawak is being run by a white guy. And to 19th-century Europeans, that's a big difference.
As for the Philippines being a western nation, that would have required that the British, French, Dutch and Americans (plus the Germans, once they unified) actually regard Southern Europeans as properly white people. At best, they qualify higher on the racial hierarchy than their neighbors, but still well below proper North European stock.
You know, I'm pretty sure the number of White Guys in the Philippines is higher than that of an adventurer-kingdom in Borneo.
I do get what you mean though; the Philippines aren't exactly the first choice an European would point to as an independent or "civilized" polity. Nevertheless, the sheer length of Spanish rule and it's effects might just swing in the Filipino's favor. Besides, there are other ways to gain influence and money without outright colonization.