I'm a bit at sea regarding the divergence of the USA getting ahold of Cuba so very early; it needs to be worked up at the very least. Some points to consider:
The attitude of Britain;
The political balance between slave and free state;
The fact that, apropos that, Cuba was not as much a slave society in the early century as it would become later--clearly slavery was not abolished (as it would be in Mexico for instance) but the sugar plantations of the later century were yet to be developed, and it was these that made Cuban slavery so widespread.
How will US society react to absorbing an island with a large, Spanish-speaking, Roman Catholic population? Will the outcome be ethnic cleansing, or the wooing away of the Cuban populace from their language and faith? Or will the Cubans perhaps react strongly upon the US identity itself? When Americans seized other Hispanic territory later in the century, they tended to pretty much displace or suppress the Latino layer--but circumstances are different here. Texas and California were distant peripheries of Spanish and then Mexican society, very thinly settled (by peoples loyal to Mexico anyway) and only recently, whereas by the 1840s the USA had grown immensely from its late 18th century origins. Here however, a much younger and smaller USA is trying to absorb a long-established and fairly populous Hispano-Caribbean island, quite a large one too. I don't think the examples of Texas and California are much good here. Even the example of New Mexico--where a strong group of Spanish-identified people live on to this day--is not really appropriate. I think it would turn out a lot more like Puerto Rico, which is of course predominantly Spanish speaking. I suspect rather more fusion of the cultures than happened there--but it will happen on largely Cuban terms.
What about Florida, by the way? How likely is it that the Yankees will get control of the old, long settled island of Cuba but neglect to seize the only marginally held continental enclave between Cuba and such American states as Georgia and Alabama?
We have to pay attention to a rather kaleidoscopic sequence of events too--one where I have come to realize, as AH challenges often cause, that I'm pig-ignorant!


Florida was Spanish, but the British took it in the peace settlements of 1763--then suddenly it was Spanish again. Was that simultaneous with the British ceding Louisiana to Spain? Why did the British abandon their claims on the southern border of the USA anyway--did they deem them not worth the cost (despite their obvious value as bases to harass the upstart colonials from), did the USA twist their arms at the peace talks (demanding the territories go to a third party rather than remain under British control) or what?
Anyway now Florida is again also Spanish, and if the USA is going to seize Cuba by main force, surely they'd sweep up Florida too? But then again--the reason Spanish Florida ever stood any kind of chance up against a bunch of greedy Americans (whom I can't exactly call "Yankees" since the proximate pillagers would in fact have been from as deep as the South gets, Georgia and Alabama--note that Alabama is just barely getting settled and probably isn't even a state yet) was that the British were backing them. OTL the Spanish would be conceding Florida to the USA anyway just a couple decades hence, and I don't recall hearing about the British opposing it. But again those couple decades represent growth of American power, and despite the quite recent second rupture of Anglo-American relations in 1812, the development of new attitudes of the British toward the USA. Jumping the gun some quarter century, I think British displeasure is going to be in play--it might not be effective, especially if they are bogged down fighting Napoleon or some such, but anyway the consequences of a US/Spanish war probably resonate far beyond just the match of power in the Caribbean sphere between those two alone. Heck, Napoleon Bonaparte might get involved!
Indeed, perhaps a seizure of Cuba might somehow butterfly away the Louisiana Purchase!
Say it happens before 1800--John Adams is President, and he doesn't want the USA to absorb Cuba. But his Federalist supporters are split on the matter, and so are the Democrat-Republican opposition; a coalition of convenience on this issue exists in Congress in favor of taking Cuba, one strong enough to overcome Presidential opposition--perhaps even in effect taking away the role of Commander in Chief of the military from the President if Adams won't get with the program. In that case I fear Adams goes down in disgrace--considering that he is only the second President this could mean major changes in the Constitution (as pragmatically interpreted anyway if not as written). Letting supreme military command slip to other hands at Congress's direction for instance (in flat contradiction of the text of course). Or establishing the principle that it is Congress that adjusts American territorial claims, not the President.
But then what happens in Jefferson's first term (assuming Jefferson got on the Seize Cuba bandwagon, or anyway stood aside and didn't let it run him over like Adams) when Napoleon's envoy offers on a silver platter (in return for some actual silver) enough territory to double the size of the USA; complete control of the whole Mississippi valley system; even access to the Pacific--but Jefferson and his party as well as some Federalist allies have just established that only Congress can handle the deal--but Congress can't act fast enough; Napoleon, hungry for money immediately, gets impatient and takes the deal off the table...goodbye Louisiana Purchase, it would have been unconstitutional to act fast enough to say yes!

Presumably the USA gets control of all or most of that territory eventually but there might have to be a number of ugly and relatively expensive wars first. And it might not permit a fast enough leapfrog to the Pacific to secure an early claim on Oregon; the Pacific coast might be preempted by the British as well as Mexico, or even the Russians might hang in.
I'm hardly saying this is a sure and probable result of an early conquest of Cuba, I'm just saying the doors of possibility and unforeseen consequences are flung wide open. The whole pattern of international politics in the Western Hemisphere is completely torn up and randomized. For one thing, the USA is certainly going to be known for military adventurousness. Will other Latin American peoples, struggling for their own liberation from Spain, view El Norte as a ravening werewolf as bad as the Castilian vampire? Or will they see the incorporation of Cuba into the Union as a sign of a new era of hemispheric Federalism, with the Anglos as cousins in a fraternal New World of collegial and cooperative republicanism?
Just about any crazy thing can happen now!
------
But while that does certainly mean that your favored scenario of the Philippines going on a different path and perhaps even being drawn into more fraternal association with Spain in permanent union might possibly happen--it doesn't seem particularly probable either. Just another of a near-infinite variety of permutations.
Meanwhile, I read your OP as somehow suggesting there is a necessary and logical linkage of some kind between Yanqui aggression in Cuba and in the Philippines. And there certainly are linkages--but the way I would bet, if the absorption of Cuba does not send either the USA or the whole world onto courses completely different from OTL but that events still proceed largely as OTL for deep-seated reasons...then I don't think that the Americans taking Cuba a century earlier has any bearing whatsoever on whether or not they are in a mood to try to conquer the Philippines pretty much on schedule.
As I have posted above, the Americans at that point, around the end of the 19th century, included some very hungrily ambitious people with imperialist notions, and this view had the backing of particularly powerful and influential Americans as well as a fair sized popular following. A place that more or less met the conditions the Philippines did OTL at that time--in or near the action of East Asia; under some kind of weak control--would draw American eyes and elicit stomach growling.
Perhaps, for random reasons, or for reasons that follow with iron logic from the failure of early 19th century Spain to hold Cuba, the Philippines no longer meet that description in the ATL. Maybe the reformist desire to get more value out of the Philippines takes hold earlier and stronger in Spain an ingenious viceroys and ambitious and clever Spanish subjects multiply their grip and start enriching both Spain and themselves--so it is an ugly, racist, iron-fisted regime in the Philippines perhaps--but a richer and stronger one that can fight off an opportunistic US battle group while handily suppressing the natives.
Or the Spanish turn over a new leaf and take another tack, and effectively recruit the Filipinos, integrating them into a more collegial empire that they have a stake in.
Or inspired by the liberation of Cuba, the Filipinos win a precocious victory much earlier in the 19th century; a combination of luck and their own pluck keeps third party vultures from swooping down on them or fights them off when they do (probably mainly by playing the colonial imperial powers off against each other) and the awakening American giant finds the Philippine federal republic a tough-looking mouthful on its own.
All of these things are possible but none of them seems particularly probable, and an OTL type trajectory does seem the path of least resistance for the Philippines.
And so the Americans might wind up seizing them anyway--and in this timeline there would be no perception of any linkage whatsoever between this case and the case of Cuba most of a century before.
--------------
Looking at other comments going on, I see that the major linkage you seem to consider relevant to the question of whether Spain can hold the Philippines is a matter of troop strength. That is--if they don't have Cuba to hold as well as the Asian/Pacific holding, they can double down on the latter and therefore hold it.
That seems dubious to me; the Filipino rising as it was evolving OTL had breadth and depth and the Spanish would have had to send in some pretty vast armies indeed to hold them down by main strength. In my nasty scenario above, the main strength comes from more Spaniards resident in the Philippines, not as troops but as locally resident magnates of a successful colonial mini-powerhouse--some sort of Draka-apartheid sort of nightmare, but while a Spain these honorary Peninsulares help enrich can afford to send more force, some of it also comes from the islanders themselves, coopted into an imperial hierarchy--one opposed, probably, by an insurgency, but perhaps one that never overturns the hierarchy.

Here, avoiding such hyperbolic if dark fantasies, you seem to be dealing in essentially as OTL but with more Spanish boots on the ground. IMHO, that just escalates the fight, but the native people will win--and if the Yankees aren't butterflied away or onto a different path, their white fleet is lurking right there waiting for the rebels they perhaps have aided to pull American chestnuts from the Spanish fire--and in comes some ATL cousin of Dewey to eat them.