A major reason the USA did take and hold the Philippines--at some considerable cost, which everyone who assumes some European colonial power or Japan would just swoop in and own it outright is discounting implicitly here--was that the Navy, and American business interests, wanted an outpost to get at trade and hold strategic positions. In other words, just as with the original Spanish conquest centuries before, the idea was not to obtain and profit from the islands themselves so much as to get access to more valuable goals--particularly China. Centuries before, Spain needed a foothold near China that could be approached from the east, because they were barred by the Papal-mediated Treaty of Tordesillas with Portugal from coming from the west--that was in the Portuguese hemisphere. The Philippines were on the Spanish side of the great circle the Pope had selected to separate and settle Spanish and Portuguese spheres. The Spanish never were able to greatly develop China trade as they hoped but they did have some, from Chinese merchants who sailed to and sometimes took up residence in Manila. The Yankee goals were largely an echo of that same sort of calculation; developing the Philippines themselves was an afterthought.
Thus, I think there was another option available besides either trying to conquer the islands completely and wholesale or sailing away and letting them take their chances with all the colonial sharks circling around. Those colonial powers, had they tried to take the islands themselves, would surely have run into the same buzzsaw of resistance the Americans did--but to be sure, the Americans did eventually win peace in the Philippines, and I guess with the right combinations of ruthlessness and judicious co-option of locals the Germans, Japanese, French, or British might have been able to settle matters. Just saying it would not have been a cakewalk; the Filipinos had been waging revolutionary war against Spain for some years and Spain was in some danger of being thrown out anyway.
But suppose that instead of ignoring Filipino homegrown political institutions and setting out to impose wholesale colonialism, the Americans had negotiated and won the right to big bases and some concessions in the Philippines, in return for a guarantee of Philippine independence from all comers? Basically the right to develop Subic Bay as a naval base, plus a good shot at capitalist investment in Philippine development across the board.
My impression from some rather lengthy studies I did on the Philippines is that the locals might well have come up with a fairly decent government, and the USA would be spared a lot of costs, economic, political, and in lives if we didn't try to own the country outright but let them run their own affairs their own way. In practice I imagine the USA would wind up being very dominant, but that moreso perhaps than other places Filipinos would manage to turn the semi-colonial situation to their own advantage even so. There might have been fair chances for profit for all, enough to go around, and the American military presence there could concentrate on their more grandiose missions knowing that the Filipinos valued the deterrent effect of a large American presence there and therefore their home port would be safe as long as the Americans could keep any strong foreign powers from invading. Until 1941 no one would want to bring the full power of the USA down on them even if they could overwhelm the fractional American power actually present in the Philippines plus whatever resistance the Filipinos could muster on their own behalf.
Which, I want to stress against, was surprisingly much.