Ok so, in Spain, you have a goddamn mess. Assuming in this scenario most of Isabella and Ferdinand's children survive their childhood's but die decently young, you might even kill off Isabella earlier than OTL. But let's say she manages to survive until 1504, just for consistency's sake.
These are the deaths I'm going to go ahead with:
- Isabella of Aragon (b.1470) dies pretty much the same as OTL, and Miguel de Paz follows suite.
- Juan, Prince of Asturias (b.1478) also follows the same path, including married and posthumous stillborn daughter with Margaret of Austria.
- Joanna of Aragon (b.1479) dies shortly after arriving in Burgundy, in an illness that also takes her husband.
- Maria of Aragon (b.1482) dies during her pregnancy with OTL John III of Portugal.
- Catherine of Aragon (b.1485) dies in 1501 of the same illness that took her husband, Arthur Tudor, Prince of Wales.
Between 1497 and 1502 all the young people are dead.
What now?
Well, some sources claim Ferdinand proposed a marriage with Juana of Castile (Joanna la Beltraneja) around the time of Isabella's death, and here, even if she doesn't accept it, she could still take the throne where she has no real competition. Ferdinand is likely to just claim it all for himself anyway, but maybe she would be able to take power. At 42, she's unlikely to have any children, Ferdinand or otherwise (although it isn't an insane prospect), and considering she didn't accept this alleged suite, let's assume she rebuffs him again. They end up in yet another major war for Castile, and if she does win, then she's got a long time before her OTL death in 1530 to set upon an heir. OTL she apparently favoured the
King of Portugal, so we might see that here.
Ferdinand, in a scenario where he's completely lost Castile and is unattached, is likely to do what he did OTL and marry a French Proxy. If he doesn't look to France, Portugal has an option in Manuel's niece by his sister Isabel, the Infanta Catarina of Braganza (if she actually existed, because it's hard to find firm evidence one way or another). But honestly, Germaine of Foix makes the most sense. Unless he marries his niece. But that's gross and I'm going to ignore it as an option.
What I'm not going to ignore is that his niece is probably his heir in this scenario. Joanna of Aragon isn't about to marry and produce a male heir at 49/50, so Joanna, OTL never to marry again after her weird incestuous marriage to her nephew. Here, she probably gets to marry a second time to whoever they can find that Ferdinand would be ok with with. My best bet is that she marries Gaston of Foix, Germaine of Foix's brother, in maybe an alternate pro-French match that also adds legitimacy to Ferdinand's Navarrese ambitions.
Now it's time for outside of Spain.
In England, Henry VII needs to find a bride for the future Henry VIII now that Spain has no easy descendants of Philippa of Lancaster to offer. Again, if Catarina of Braganza exists, she's a good option. They might, try for Margaret of Austria or Sibylle of Bavaria. Most likely, that dream is given up entirely and Henry is betrothed to whoever makes the most sense politically. Probably someone like Anne of Navarre.
In Brussels, if Philip of Austria is dead, then the widowed Margaret of Austria is
Duchess of Burgundy and the only option left for Maximilian if Bianca Sforza isn't going to have a surviving child. If the marriage with Savoy even happens, it's unlikely to be her last, and she may end up with her Bavarian cousin. She could also consider an English match. It's unlikely, but if nothing else it'd be interesting.
Now for Manuel, the world is pretty much his oyster, but he also needs to move fast. He's had two brides die one after the other, and there's no obvious domestic brides (except the elusive possibly imaginary Caterina). I can imagine him pushing for Joanna of Naples, but maybe after two attempts he's unsettled by the Trastamara brides and goes elsewhere. I'm not sure where he would look in specific, Mary Tudor is too young, there's no French brides available that won't be in contention elsewhere.
Weirdly enough, I can see Kunigunde of Austria's Bavarian daughters becoming surprisingly big prize brides in this scenario, just because there's a distinct lack of royal women available from the regular big guns. Also the Navarrese girls.