A ship is nothing without its gran Admiral, which Don Alvaro died just at the start of the invasion, unfortunately.
But still even with the best ships Portugal got PU'ed
I fail to understand this post of yours.
Yes, Portugal did accept a Spanish King if you do mean that. The cortes (in Portugal) accepted Filipe II of Spain. We (Portugal) had a bastard trying to get control of the country but he was still a bastard and didn't have the support of everyone. That is the only reason Spain actually crushed this pretender rather easily, otherwise it would have been Aljubarrota 2.0. Or an earlier Montes Claros. Almost all Spanish-Portuguese engagments ended in defeat for Spain, despite the colossal difference in resources and men. I don't think it would have ended differently, if the proper support was put behind the proper man.
Also you seem to have trouble understanding war. Spain invaded by land. Ships can't fight in land. Portugal isn't an island like England - if Portugal was an island, even with the small support António Prior of Crato received, he would have won the war easily (if he had managed to secure the entire Portuguese fleet after assuming control). Spain by then was still determined on following the old way of fighting at sea by boarding ships. One of the main reasons why they got beaten so badly by the english. And why Portuguese ships couldn't do much by themselves.
You probably also fail to realize that the Portuguese actually aided the Spanish army/navy in fighting Antonio Prior of Crato but after all the comments I have seen in here and in other threads I would not be surprised.
Check
https://en.wikipedia.org/wiki/Conquest_of_the_Azores or
https://en.wikipedia.org/wiki/Battle_of_Ponta_Delgada for instance. Check the other belligerent nation fighting on the Spanish side. You might be surprised! You probably do not know but the oceanic galleons (on the Spanish side) leading the fighting in both those fights were all Portuguese. If Antonio actually had seized all of the ships, not even your Great admiral would have been able to move a finger. From wikipedia:
"
the Portuguese oceanic fighting galleons, were precisely incorporated into the Spanish fleet, and leading the fight (despite being only two, they would be decisive, being the other ships Portuguese and Castilian carracks, urcas, and pataches). These galleons were also strongly armed—with its personnel and specialized
bombardeiros or
artilheiros—more suitable for such a strategy in the Atlantic high seas than other naus and galleons of more mixed-use, or the galleys (the widest Spanish resource for naval engagements until then)"
Also, I would like to point out that the disastrous changes to the Portuguese ships were actually ordered by Alvaro de Bazan. The Great admiral you actually speak of. The Portuguese ships were not designed for boarding, and the changes, as I said made them extremely vulnerable, slow and hard to maneuver. The Portuguese had been fighting their naval battles all the time and winning most of the time merely with their artilery.
But yes give the artilery bonus to Spain, Paradox! And not even one single bonus to Portugal, the ones who were better than the Castilians in naval warfare (in open ocean at least).
Taken from
https://en.wikipedia.org/wiki/Battle_of_Ponta_Delgada. Probably not the best quote but the only one I could find with my limited time. Might add more later, or not.
"In spite of the effective use of artillery, the battle was largely decided in the traditional style of boarding the enemy,
although the Portuguese were the first to understand the importance of naval artillery. Apparently, Strozzi ignored the
Portuguese who were in his fleet and recommended the use of artillery in their line of battle tactic, as they were doing in the Indian Ocean (resolving many battles by gunnery alone), and who would be adopted by the other Europeans in the 17th century"