Was there constant (near-daily) travel between the Philippines and Mexico? How did taxation, trade, and communication work? Would an event like the Mexican Revolution have taken weeks to reach Manila? Did there exist much social or institutional continuity across the Asian and American possessions of the Spanish Empire? Would a Spaniard setting in Mexico or Cuba have the same legal opportunities if he settled in Luzon? Last, how were indigenous peoples affected by this arrangement? Did many native people from Mexico or the Philippines cross the Pacific to live under Spanish rule somewhere else?
The Spanish empire was built to deal with such vast distances. The most important point was that local officials had wide latitude to deal with specific administrative and judicial matters. On top of that there was a hierarchy that meant that tough decisions could be pushed upward to someone with more authority before it had to go all the way back to Spain. So for example there were local magistrates in the Philippines who could deal with most matters of local justice. There was a high court and governor that could deal with judicial cases and administrative issues, not to mention a whole religious hierarchy that managed religious affairs. Tough decisions could be sent to the superior court in Mexico City or to the viceroy there. In many cases, officials would implement a policy and send a request to their immediate superior or to Spain to have that policy confirmed by the king and Council of the Indies. That process could easily take 2 years. It was also normal to send out officials empowered to review the performance of existing officials. Even though communicating took a long time, letters were constant. What that meant is that there was a 2+ year delay on any specific issue even if letters and orders were going back and forth constantly.
Big topic.
The Manila-Acapulco route was usually one or two galleons going in each direction every year. Think of the Pacific sailing route as a gigantic clockwise current. The westward route to the Philippines was far easier than the one back to Mexico (about 3 months to Manila taking the Pacific's tropic current while it took ~4 to 6 months to get back to Mexico by way of the northerly and eastward Kuroshio current). Ships typically arrived in Manila in April/May, ships sailed out to Acapulco about June/July.
One main difference between Spain's American possessions and the Philippines was that, because of the distance, far fewer Spaniards went to the latter. Much of the administrative machinery was therefore run by religious orders whose friars were often the most visible Spanish presence in the far flung archipelago of 7,300+ islands.
Also, the Philippines was conquered decades later in the Spanish timeline than Mexico or Cuba, meaning the Spanish monarchy's reining in of the conquistadors with new laws for the protection of the natives was further advanced. The prospect of enrichment through pillage was more subdued. Nonetheless, encomiendas and land grants were still granted to Spanish soldiers and private citizens, though, as these expired after 2 generations, more and more of the lands passed to Crown and friar administration.
The prospect of wealth for hopeful Spaniards became more and more through participation in the galleon trade, trading from Manila for Chinese goods to send back to Mexico. One effect this had was that the native Filipinos were spared the harshest aspects of Spanish domination as expressed in, say the Caribbean in the Bartolome de las Casas' youth or in Potosi. Spaniards' private attempts to enrich themselves through large landholdings were over time redirected to efforts at trading ventures concentrated in Manila.
Not that it was fun and games for the Filipinos anyway. Population declined by maybe a third in the first half century of the conquest because of new diseases brought by greater outside contacts as well as from Spanish depredations.
Since most of the galleons over the course of the 250 years were built in the Philippines, labor had to be conscripted for them in the archipelago. An estimated million and a half people lived scattered in the Philippines' 7,300+ islands in ~1571, mostly in communities of 30 to 100 families. It took 6,000 to 8,000 able bodied men to build one galleon, dragging the truly massive hardwoods out of the jungles and building the biggest ships in the world on the shores.
This was organization on a scale not seen before the advent of the Spaniards. Labor conditions were usually terrible. Mortality rates were bad and the deaths of the men often also meant the starvation of their families. The naval conflicts with the Dutch for most of the 1600s made things worse as the Spanish exacted more shipbuilding works from the Filipinos as a result.
Oh and yes, many native Filipinos, who made up a large part of the crews of the galleons, jumped ship in Mexico. Their communities were largely absorbed into the local populace over time.