Portugal did many times try to gain the Crown of Castile, best chance is the survival of Prince Afonso, the son of John II, because all records show that he had the support of the Portuguese Nobility and this is important in case the Nobility of Aragon and Castile decides to deny either his wife of his possible sons the right to the Crowns.
Greatest effect that this would have is that this new Power would keep the Portuguese tradition of avoiding wars in Europe, while focusing in exploring Asia, the Americas wouldn't be a priority but the usual to do in those circumstances would be to sell charters to privates to explore and conquest.
The wars in Asia will go much better for the Crown with the extra manpower and resources and plans that took years to implement would be finished faster with the much needed extra ships and men. Another problem solved would be the silver crisis, has no doubt that someone would find the Inca and the Peruvian silver mines, best shot for the Incas is that they are treated like the Kingdoms in Africa establish some feitorias to have access to the silver, worst is the heavy hand treatment of just sending the army and navy in strength to ensure that they are vassals of the crown and the establishment of forts in the major cities and mines, and the creation of Iberian settlements in the coast.
Brazil would probably evolve like OTL and Mexico I suspect that it would probably end like OTL.