Interesting...
I guess I'm not sure, but might have European colonization in the Americas gone differently? I think I've heard about some explorer who attempted to solicit financial aid from the Argonese and Castillian crowns, but was turned down because of the lingering tension between the two. It's probably just a old folk tale, but could united Kingdom of Hispania lead to an earlier discovery of the new world? What would be the effects?
Doubtful. Having Castillia as a rival of Portugal rather than a friend would have made it focus on the Aragonese Mediterranean expansion. Any such explorer would have been rebuffed by Isabella.
Portugal's path of expansion would remain naturally Brazil, not America*, except that in this situation, Brazil would be only Portuguese, no Castillian colonies. An earlier discovery? hmmm maybe that explorer would have been seized up an executed, if he turned up in the Portuguese court

Archaeological evidence shows that there had been Portuguese shipwrecks on Brazilian shores since late XV century. Maybe they had knowledge of those lands, but wanted to keep them a secret resupply base.
Would the Incan and Aztec nations be marginalized by a stronger colonization effort, or would they be able to resist encroachment like in OTL?
An earlier arrival of the Europeans would have made things better for the native kingdoms, not worse: they would be confronting Europeans with poorer technology, and worse capability to adapt to the tropical environment. Also, it would give them longer times to adapt to the European diseases.
Also, would the rest of the peninsula been united under the same crown? Would we not have an independent Navarre, Portugal or Granada?
I can see Granada and Navarre being swallowed up by Castille. Remember that Granada's help to the Juanistas was invaluable: if the war had turned the other side, the Nazarites, being enemies and muslim, wouldn't have survived a minute longer.
As for Portugal, only as a personal union. Castille and Aragon together didn't have the military strength to put Portugal down.
*OOC: i'm assuming that in TTL Brazil and America are 2 geographically different entities, South America vs North and Central America. Probably a rather simultaneous discovery at very distant places that made everybody think (quite reasonably actually) that it was 2 different landmasses.