The Philippines if the USA already owned all of North America

The question is what would become of the islands of Palawan, Romblon, and Masbate (all geographically part of Luzon) and the Visayas (Panay, Negros, Cebu, Bohol, Samar, Leyte, Siquijor, and Camiguin)? These islands aren't strong enough to be on their own since these do not offer much resources aside from a few farming, fishing, and lumber. My guess at some point either Luzon would start to expand or the Sultanate of Sulu in Mindanao would make them as outposts. Remember in the 1500s-1600s, Muslim pirates and bandits used to attack coastal settlements in the Visayas hence why there are forts and watchtowers by the coastline. Though these pirate attacks died down by the 1700s, I'm sure the Sultanate would want to have a foothold in the Visayas.

You might need a different PoD for the US to even absorb all of North America in this case, though your typical classical "US Wins War of 1812" comes to mind. However, absorbing Mexico might be a bridge too far due to the historical anti-Catholic sentiment there (even when the US would later open its doors to Catholic immigration from Italy and Ireland in this case, as well as parts of Germany that remained Catholic).

Yes, I do apologize for the whole "Imperial Germany as proto-Nazis" thing, though I forgot that other nations had practiced the whole 'exterminate the natives' thing, especially the Russians with regards to the Circassians and the Americans towards the indigenous populations there. What I could predict with a German colonial administration in the Philippines might be a German equivalent of the Thomasites coming into the Philippines and reforming Philippine education there. I also think that you might also have some limited amount of industrialization happening there, as well as Prussian style of behavior (military service leading to civil service and German behavioral values like efficiency and punctuality). I shudder to think what a German-trained Philippine colonial troops might be like in battle.

Well, a suitable event sequence for the USNA may vary, but I have a few ideas. By the way, I wrote one with a description of ATL changes in this scenario, in the OP. It is not my fault (and a source of some considerable frustration) if people do not bother to read it and jump in the discussion after taking a glance at the title and assuming the topic is about a 1898 PoD. Perhaps I should have picked a different one, such as "The Philippines if the USA already owned all of North America".  

For various reasons, IMO it is best if it starts with settled Canada joining the Patriots in the ARW. Political variables make the British colonial administration of Quebec and Nova Scotia oppressive, and the Quebec Act as bad for them as the other Intolerable Acts were for the 13 colonies, driving them to rebel and send delegates to the Continental Congress. Newborn America takes Middle Canada and the Maritimes in the peace settlement. For simplicity, let's assume PEI stays British or a part of NS (too unbalancing to US federalism otherwise), and Acadia/New Brunswick later separates to become a state like Vermont and Maine. The Canadiens find their comfy place in the American system with a few harmless guarantees in the US Constitution about their religion and language. Their partecipation in the American Revolution makes anti-Catholicism unpatriotic and politically taboo, and it builds a powerful precedent for inclusion of more Catholics and Romance-speakers in the American experiment. For even more inclusiveness, the leaders of the Iroquois Confederation have a leap of insight and ally with the Patriots. This makes American society tolerant and willing to integrate friendly 'civilized' Natives that do not oppose US expansion and embrace the American way of life. It creates a path to assimilation that the Five Civilized Tribes, other siimilar groups, and the Europeanized natives of Mexico and Central America are later able to follow. Of course, Native tribes that resist US expansion and cling to their traditional lifestyle are crushed as brutally as usual.

Political variables keep the Federalists dominant or at least politically influential longer, and the policies they favor accelerate infrastructure development, Western settlement, industrialization, and US military build-up. The War of 1812 may or may not occur, but if it does it turns out better for the US thanks to more favorable strategic circumstances and it just makes the British even more persuaded that North America is a lost cause for them. Even if it does not occur, relentless American expansion combined with British inability to settle or defend Western Canada properly due to lack of access to the Great Lakes route makes Britain come to the same conclusion. The British accept to sell Rupert's Land and cede their claims on the Pacific Northwest to the USA. When the Latin American Wars of Independence occur, sympathy for the rebels and border conflicts with Spain drive the Americans to intervene. Spain is at its lowest ebb, and the US military is well prepared, so the Americans win and seize Cuba, St. Domingo, and Puerto Rico. They force the Spanish to concede independence to New Spain and Gran Colombia. US support for their cause builds a sizable amount of goodwill among Creole revolutionaries. This may reasonably become justification for the likes of Simon Bolivar to seek union with the USA then and there, but let's keep a more gradual pace. 

Political butterflies related to the greater amount of free states ensure the Upper South states never adopt slavery in the first place, or eventually decide to abolish it on their own initiative. The remaining slave states increasingly feel cornered, and for a while believe the solution (not for parity, that ship sailed long ago, but to stay a relevant minority) is more territorial expansion. Pro-US settlers in the northern territories of Mexico secede with the breakaway republics of Texas, Rio Grande, and California. American support to them and conflicting territorial claims cause the Mexican-American War. The Americans surely take the breakaway states, the Southwest, and Northern Mexico.

A good case could be made for taking all of Mexico then and there. The Canada, Greater Antilles, and 'civilized' Natives precedents suggest the Americans there is little to fear and much to gain from doing so. On the Mexicans' part, they can see the Catholic and Romance-speaking sections have been enjoying prosperity, liberty, and stability under US rule; this makes an eloquent contrast with the poor record of independent Mexico. Moreover, despite the recent bad blood, there is lingering pro-US goodwill from the Wars of Independence. Even if the USA leave Central-Southern Mexico be for the moment, something bad happens to it a generation later. Say a civil war, or the usual French invasion. The Americans intervene and restore peace, or kick the invaders out. In the aftermath, the Yankees and the Mexicans reassess the situation, and agree union is the best solution. 

The slavery issue gets settled in one of two ways.

a) the slave states realize the days of slavery are numbered, since the freesoilers and the antislavery Mexicans successfully resist its expansion in the West. With more and more free states further tilting the political balance, the Congress and the courts are turning out more and more antislavery legislation and rulings. The day is coming when abolition by constitutional amendment becomes feasible. The dominant free section is increasingly eager to get America rid of this moral blight and socio-economic burden. The balance between the free and slave states is so skewed in population, economic, and military terms that secession would be crushed in a few months. The slave states reluctantly accept gradual emancipation in exchange for population transfer of the freedmen to West Africa. The federal government and the free states accept the bargain, since even most abolitionists do not want to integrate the freedmen if they can avoid it.

b) the slave states assume the secession strategy may work despite otherwise very bad odds thanks to foreign support. Britain and France agree to help to cut down the US giant one notch and expand their influence in the Americas. They start the ACW, and the Anglo-French intervene to support the Confederates. The Union has a Pearl Harbor/9-11 moment, stages all-out mobilization, and crushes the slaveocrat traitors and their foreign puppetmasters. Their unholy compact to destroy America causes the Unionists to demonize and suppress slavery and all its works, including segregation by extension. This paves the way to integration of the freedmen in American society. 

Assimilation of Central America may take place in various ways: 1) filibuster takeover, the swan song of slaveocrat expansionism (successful William Walker) 2) peace-enforcing US intervention, followed by annexation (the Banana Wars done right) 3) the Central Americans can see the writing on the wall, and ask to join the Union (the 1870 annexation attempt of St. Domingo done right) 4) the Americans want to build the Nicaragua and the Panama canals, decide direct ownership is the only acceptable means, and negotiate the annexation of southern Central America in exchange for economic benefits; in the case of Panama, if Colombia does not want to sell, they just do what they did IOTL. 

This leaves Haiti, NFL, and the British West Indies. The former is such a terrible mess that I'd prefer to ignore it, and I suspect this would be the attitude of the American public. A possible alternative is the Americans get disgusted of having such a hellhole in their backyard, send in the army, and engage in an extensive and sustained effort to rebuild the place from the ground. As it concerns NFL and the BWI, the obvious solution is America taking the side of the CP in the WWI equivalent. Not worth the effort if NFL and the BWI were the main issue and prize. However, the Americans may get pissed off at British blockade of their trade to Europe and decide to do War of 1812 2.0. Alternatively, or in addition, they may well decide after they are done with North America, Australasia would be a good next step and excellent prize, and engage to reunite most of the Anglosphere under the Stars and Stripes. Take into account TTL America quite possibly fought the French and/or the Entente powers in Mexico and during the ACW, so they have less reason to be pro-Entente. Moreover, being much more multi-cultural, Anglophilia is going to be considerably toned down.

Never mind about the 'colonial atrocities' issue. It is just the 'Germans are eternal Nazis' meme (and the 'Only Europeans/Whites/Westerners did bad things' one) especially annoy me for various reasons. I agree with your broad assessment of German colonial policy. For German Congo at least, I am confident the change is going to be a genuine improvement. 

It would be interesting to see what a Visayan Republic would be like. The islands on their own aren't militarily or economically strong to be on their own so uniting the entire Visayas would make more sense. Mindanao however could fall under the entire Sultanate of Sulu.

So you're saying Visayas remains a far-flung Spanish colony (just like Hong Kong and Macau) while it shares maritime borders with Luzon and the Sultanate of Sulu?