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Spain basically gave up exactly the territories they had lost direct control of in the war:
The peace treaty specified that Cuba was to be given independence while the other territories would pass to US control.
That said, the Spanish were initially not willing to give up control of all the Philippines (nor Cuba for that matter). They were only convinced after difficult negotiations. They may have planed to reconquer whatever territories they would retain from the Filippino revolutionaries later, or they may have planned to sell it, as the US delegation anticipated. This is exactly what they did with the rest of the Spanish East Indies when they sold it to Germany in 1899 for 25 million pesetas. In fact, warships form several other countries (especially Germany) had been present in Philippine waters during the war, waiting like vultures if there would be any leftovers for them to seize and turn into colonies after the war (which they might have done in case the Philippines would have been left to the Filippino revolutionaries as an independent republic instead of being occupied by the US).
This leaves the question, why did the US want Guam and not the rest of the islands. Guam had been an administrative hub of the Spanish colony, an important port of call for voyages between the Spanish colonies in the Americas and the Philippines. At the start of the war, the Americans were apparently under the impression that it was a mighty fortress. So Captain Glass had orders to seize it with his flotilla on his way to the Philippines while not bothering with the other islands. When he got there, he found the defenses in a sorry state and the Spanish garrison utterly unprepared to defend anything (and unaware of the existence of the state of war between Spain and the US).
Later, Guam was seen as a strategic port and military base in case of a war with Japan and a logistic waypoint to East and South East Asia.