Well, John claimed the throne of Navarre, but the rightful heir was Catherine, daughter of Gaston of Foix, because Navarre didn't have Salic Law. One thing you could is to make Francis I of Navarre live longer and marry a daughter of Isabella and John. It would unify their claims of Navarre and their children would have a claim on Castille.
The union of Aragon and Burgundy would still need to face French oposition. France wanted Burgundian and Aragonese territories, but now they don't have the resources of Castille and the HRE to help them. Aragon would be desperate to find allies against the French. You could see an alliance with Portugal and Castille (as Juana is married to the Portuguese king) and whoever is an enemy of the Valois. Could England enter this alliance too?
Yeah, you're right about Catherine, however I still think binding Castille and Navarre closer could eventually end up in a Union, not through Isabella and John though. Right now Castille, Navarre and Aragon- Burgundy are creating a block while France and the Habsburgs are creating a rival block. With Maximilian's marriage to Marie of Orleans has brought the HRE and France closely together. Portugal is against Castille for the moment at least, and England is for the moment not associated with any of the blocks. However the early deaths of Mary could probably create more trouble...