AFAIK Castile and Aragon were still different kingdoms until the Nueva Planta decrees that abolished the Aragonese institutions, why were the colonies created in the Americas part of Castile and Aragon didn't had any as part of them exclusively (ruled and administrated by Aragon only)?
Many people often discuss monarchy or imperial style government and administration as a single entity. The king/emperor is the head of the entire state, for example. This explanation does not get into the nuts and bolts of governing, however. The English system, for example, relies on cooperation between the monarchy and its subjects of various classes. Its development took centuries to evolve into Henry V’s realm which would have not recognized the realm of the Hanoverians a few hundred years later.
This process is just as relevant for Iberia. The Spanish-speaking kingdoms (which is a problematic description, I grant you) each developed into its own unique monarchy. Those states had legal, ecclesiastical, and political cultures that did not always reflect the ones of their neighbors. Castile y León developed a monarchy that while ruling with the consent of the people, was able to use medieval tradition and local law to act with more absolute power than Aragon to the east and Portugal to the west.
Continue down that road and the Reconquista makes more sense as well. When Castile reclaimed lands administered by the Moors, it rewarded the soldiers and land claimants with status. That status usually came in the form of political and administrative power in the form of town councils or the kingdom’s assembly, the Cortes. Castile was consolidating power at the local level by rewarding allies with status in exchange for a continuation of absolutist power against Moorish occupation. Aragon’s development in the east did not follow this pattern of reconquest and resettlement of traditional territory. Aragon moved further into the Mediterranean into new lands. Castile’s power as a monarchy works within this model of conquest and consolidation.
When the first voyages left Iberia for the Americas, they left from Castilian ports, not Aragon. Most of the crews were Castilian, not Aragonese. Those ships moved west, into traditionally Portuguese waters which was a shot across the bow (sorry) fired by Isabel of Castile rather than her husband Fernando of Aragon. Therefore, any lands found would be seen as an extension of Castile itself. Even when men and women from all of Charles I of Spain/V of HRE’s realms went to the Americas in major waves starting in the late 1520s, those American territories were still seen as part of Castile. The absolutist tendencies of the Castilian system also worked better in the Americas. Aragonese systems still had to negotiate with Christians and occasionally Muslims who behaved in ways that the Aragon system could understand in the Med. Legal and monarchical traditions were deeply ingrained. In the Americas, however, it was literally the Wild West. Firm, authoritarian administration from both the church and state was needed to negotiate new cultures, traditions, and concepts of political order. Castile’s loose style of “beg forgiveness instead of asking permission” during the early years of conquest was effective. It made post-conquest development more difficult however. Those same men who helped bring down the Nahua kingdoms in Mesoamerica and the Inca in the Andes expected to be rewarded as their Castilian ancestors had. By the end of the 1500s, Spain’s monarchy had organized new structures and administration to govern the Americas in a way foreign to the traditional Castilian model.
To sum up, it was easier for the Spanish Crown to begin conquest and settlement using a Castilian model. Once the authority of the Council of the Indies was in operation by the 1520s, it no longer mattered what claim Aragon might try to make.
Elliot’s “Empires of the Atlantic World”
Gongora’s “Studies in the Colonial History of Spanish America”