Before Mary, Queen of Scots' execution, Philip had prepared to invade England to dethrone Elizabeth and enthrone Mary. Mary, who had Tudor blood, had a good claim to the English throne and so her enthronement would fulfil the Pope's deposition of Elizabeth and ensure England returned to Catholicism.

Mary's execution did not alter Philip's intention to invade, as another reason he wanted to overthrow Elizabeth was that he saw England in the 1580s as the main challenger to Habsburg ascendency. Elizabeth was supporting the Dutch revolt against Spanish rule; Philip had no hope of subduing the Netherlands until England stopped supporting her and this could only happen with regime change. English privateers were also harassing Spanish trade, which could only be stopped upon England's fall.

On the subject of James VI, Philip viewed him as an illegitimate king because he was a Protestant and claimed the Scottish throne for himself (he had an arguable hereditary claim and claimed that Mary Tudor had left it to him in her will).

However it would be wrong to say that Philip's plans were cut and dried or pursued with a consistent, determined single mindedness. For one of Philip's recent biographers has caste doubt upon the whole 'enterprise of England':

“Neither the king nor anyone else was quite sure what it was meant to achieve. No concrete plans were ever drawn up, either military or political, on what was to be done should the invasion succeed”.—Henry Kamen, Philip of Spain (New Haven: Yale University Press, 1998), p. 276.

From the evidence, it seems the negative aims of the Armada (overthrowing Elizabeth's Protestant, anti-Spanish, pro-Dutch regime) outweighed the possible, positive aims (the enthronement of Philip as England's king).

Sources: G. R. Elton, England under the Tudors (London: Routledge, 1991). Henry Kamen, Philip of Spain (New Haven: Yale University Press, 1998).

To add to the reply of /u/cub1986/ , the initial "Master Plan for England" was for Mary Stuart (Queen of Scots) to be married to Alessandro Farnese, the Spanish commander in the Low Countries. This master plan came about in late 1585, after Drake's invasion of Galicia. Prior to this period, Philip was much more concerned with France than he was with England. Mary Stuart was considered to be an ally of France, thus Philip indirectly supported Elizabeth against what he saw as French design leveraging Mary Stuart. In the other theater, he was concerned with the Ottoman threat in the Mediterranean.

What changed this view were:

1. Drake's attacks on Iberia, and attempts against the Spanish Atlantic empire. This turned England from a local nuisance into a global threat. Thus, the cost of defending Spanish interests around the world is perceived as significantly outweighing the cost of offense to neutralize the English threat.

2. Elizabeth's increasing assistance for the Dutch rebels. As late as early 1585, when asked to consider invading England, Philip II replied to Pope Sixtus V that, "doesn't [the reconquest of] the Low Countries seem outstanding to them? ... The English idea seems to lack substance." But Elizabeth's assistance to the Dutch put the English idea on the forefront, as it is seen then as a necessary conflict before they could tackle the Dutch problem.

3. France's descent into religious wars.

4. Ottoman conflict with Persia.

When Mary Stuart was executed in February 1587, all momentum had already necessitated war, and there was no turning back. England was considered to be a weak land force, with no fortification in the trace italienne style. The only fort of substance was the Tower of London. Thus, all parties in Spain were confident of victory if they were able to land hardened Spanish troops on English shores. The lack of detailed plans is also due to lack of secrecy in the Spanish court and camps. Farnese himself apologized to Philip II that he is not able to share exactly his invasion plan, lest it be compromised. This is not to say that the Spanish lacked a plan at all. So on this account most disagree with Henry Kamen's style of determinism.

Source: G. Parker, "Imprudent King: A New Life of Philip II," ISBN 978-0-300-196535, 2014.