The Inquisition under Isabella and Cisneros (Archbishop of Toledo), both reformed and rejuvenated the Catholic Church, also providing a strong base for unity in religion. The Inquisition as well as the acquisitions of the powers of church appointment from the Pope (1496) also established the Crown's control over the Church, strengthening it both politically and financially (as one-third of all tithes as well as the cruzada) now accrued to the Crown. Any move that strengthened the power of the Crown can be seen as a move for unity.
However, even in this apparent success in the religious spheres, there were elements that worked against genuine unity. The forced conversion of the Moors led to doubts over the sincerity of their conversions and continued discrimination against them laid the seeds for future rebellion. The Inquisition itself, though successful in Castile, faced limited success in Aragon due to strong resistance from the powerful Aragonese Cortes.
In terms of administration, the monarchs made many reforms that strengthened the power of the Crown, thus laying the foundations for unity. The Hermandades, something akin to a local army under the power of the crown, not only restored order in the countryside, but also acted as an effective threat against intransigent nobles. The political power of the nobles was also reduced by their exclusion from the bureaucratic machinery. The monarchs instead chose to govern via letrados, lawyers picked for their ability and loyalty, not their rank. These letrados ran the instruments of government, such as the Councils. The administrative independence of towns was also curbed by the appointment of corregidores, local officials directly responsible to the Crown who took charge of all judicial and financial matters.
Thus the monarchs laid down the foundations for a powerful administration that could provide a base for genuine unity. However, one should note that many of these reforms were only carried out in Castile. Aragon retained its separate constitution and its Cortes remained powerful. The Crown remained weak in Aragon: this weakness is epitomised by the oath of allegiance that Ferdinand accepted from the nobles of Aragon which indicates that the Crown in Aragon was so far from being absolute that it was virtually constitutional, "we who are as good as you, pledge our acceptance to you who are no better than us, as our lord and sovereign king, provided you respect our liberties ... "
In the economic sphere, the division of Castile and Aragon, despite the union of their monarchs, is even clearer. Castile was enjoying an economic boom, due largely to its burgeoning wool trade, whilst Aragon was suffering from an economic decline, due to a Catalonian revolt which had crippled its textile industry. Even the empire of Spain was fractured. Aragon's traditional sphere of influence was in the Mediterranean. The trade of the New World (ie. the Americas) however, which began under the monarchs with Columbus' discovery of the Americas in 1492 was a wholly Castilian affair, with a trade monopoly in service that even excluded the Aragonese.
In fact, the only measure of economic unity in Spain was in terms of their coinage. In the last decade of the 15th century, the three principal coins of the realm (Valencian, Catalonese and Castilian) were made equal in terms of value and even this measure seems purely symbolic.
Socially and culturally, Castile and Aragon also remained two distinct entities, with different languages and cultures. Castilians were generally considered a crude, land-bound and rather xenophobic people, whereas the Aragonese were traditionally merchants and avid explorers in the Mediterranean with a multicultural outlook. In fact, the rise of Spain in the sixteenth century, which the Catholic monarchs are said to have laid the foundations for, can largely be seen as the rise of Castile, not Aragon. For it was Castile's economic boom and larger population as well as its links with the New World that led the way for Spain's rise.
Ferdinand and Isabella united their realms in a physical sense, and created a geographic expression that appeared to denote a united Spain, especially with Ferdinand's conquest of Spanish Navarre in 1612 as well as his diplomatic manoeuvring via which marriage, which laid the foundations for the annexation of Portugal later in the century.
However, this mere geographical unity did not connote true unity. Regionalism prevailed, Aragon and Castile remained separate entities both economically and culturally. Even the annexation of Portugal was eventually bound for failure. Although they did not create a genuinely united Spain, Ferdinand and Isabella did lay the foundations for union, creating an "embryonic" (Elliott) union that would gradually take shape over the centuries. However, one should also consider that the "unity of their persons transcended the divisions of their realm" (Elliott) enabling Spain, despite a lack of "genuine" unity to be at least perceived in terms of a unity in Europe after their union.
