Some interesting butterflies here.
The immediate effects, I guess, are:
- Spain is not united, because it effectively was born from the personal union betwen the Castillian and Aragonese Crowns under one monarch. Now we have the entire peninsula
except Aragon united under the scions of this marriage. Depending on the personal interests and affiliations of the future Portuguese+Castillian King... we might see a more Castillian Portugal or a more Portuguese Castille, either which is a fascinating scenario, in my opinion.
- Inexistent Spain has no business in Italy... I might be mistaken, but if I recall correctly, the claims the Spanish monarch had on Italy derived from their Sicilian interests (which itself came from Aragon, not Castille), and it was enough to oppose the French invasion under Charles VII which sparked the Italian Wars. Obviously, Aragon itself will be interested in securing their Italian possessions, which will put them in conflict with the French (specially considering they already had a lot of "bad blood" against them since the Sicilian Vespers).
- Again, I might be mistaken, but it was due to Isabella's support that the Spanish monarchs financed Christopher Colombus' voyage. Perhaps, if she convinces her husband Alfonso V, the Portuguese will be acclaimed with the discovery of the Americas
Finally, considering that IOTL Ferdinand and Isabella had but one daughter (Joan "the Mad"), who married the Habsburg son of the Holy Roman Emperor, Spain doesn't gets under the hold of the Habsburgs... which itself butterflies away a lot of 16-17th Century History... perhaps the Netherlands doesn't even comes to pass (because the country appeared united against the Spanish oppression).