>I would argue with Manila the Spanish actually kind of did both.

Sure.

>Now I wonder if this low priority on trade has not had adverse consequences for the modern Philippines after independence from Spain

The Dutch profited immensely from intra-Indonesian trade conducted by native Indonesians. Perhaps the Spanish were less opportunistic and more restrictive and controlling.

But it is always difficult if not impossible to draw proper causal inferences from such observations.

In any case, internal trade is likely to have had a more lasting impact than the regular but sporadic galleon trade.

I am not saying that trade wasn't important, but on the whole Spanish rule in the Philippines was not profitable and depended on substantial annual subsidies.

Also, if the goal was mainly trade the Spanish could have made use of Manila similar to how the Portuguese and Dutch used Malacca and Batavia during the 17th century: as trade hubs and chokepoints to control, dominate, or divert existing trade routes - without caring too much about conquering the hinterland and converting the native population.

Other examples of this approach are Ormuz, Goa, and Macao (Portugal) and Bombay and Calcutta (England).

I think the Spanish approach was quite different from the start and that it is fair to say that trade was not their main priority even in the Philippines.

A lot of history is generalized - especially when it comes to broader claims.  

As to your question "Did the Spanish empire focus less on trade than the English and Dutch," the very short answer is "yes." The longer answer is "It depends on place and time." 

Let me explain. 

In general histories, the English empire is (more or less) India, the Dutch empire is Indonesia, and the Spanish empire is Central and South America. (Which also means that the Philippines hardly feature in the more general treatments of Spanish colonialism.)

Generally speaking, imperialism in Asia was initially aimed at trade with wealthy and productive native societies. Large-scale conquest was at first impossible and only occurred at a later stage. 

In the Americas, the situation was different. Population levels were lower (although this was not the case everywhere) and native societies enjoyed a lower level of economic and technical development. As a result, imperialism in the Americas was more aimed at conquest, the establishment of European settlements, and resource extraction. Native societies in the Americas did not by themselves produce much that European buyers wanted.

As and added factor, Spanish colonial trade was generally subject to stricter and more limited monopolies, and did not create wealthy merchant elites to the same extent as in England and the Dutch Republic.  

But please note that there will always be exceptions. English colonial settlements in New England also do not fit the trade-first pattern. European settlements in the Caribbean were all about trade (sugar), but not with native societies.  Etc., etc.  

Finally, based on my very limited knowledge of the Spanish conquest of the Philippines, I would suspect that this fits better with the “American” pattern than the “Indian” or “Indonesian.” 

Hope this helps.