I'd say the Revolt of the Comuneros was more reminiscent of the old anti-feudal revolts than anything geniunely democratic. After all, their main goal was to ensure Juana ruled. Despite her mental instability, many say she wasn't actually as mad as many think, but rather because of her depression and such, a variety of men, from her husband, to her father, to her son, were able to take advantage of her. Of course, this revolt is likely to take advantage of her as well if it succeeds; she seemed to know this, as she refused to work with them or sign any of their Edicts.
Maybe we see her recognized as indisputable sovereign of Castile and Aragon if she does go along with it (the Revolt of the Germanies was happening in the same period -- maybe they could link up?). We'd also see Charles' and his Flemish retinue forced out, and perhaps Juana is forced to recognize Ferdinand as her heir rather than Charles. That was something that Ferdinand of Aragon wished, as Ferdinand, his namesake, had been born and raised in Spain.
I disagree. Their main goal was not to ensure that Juana ruled. Their main goal was to ensure that the Cortes ruled and the old law inspired/based on the Partidas was respected. Juana was seen as the mean to ensure that since thre was a need of legitimation through a royal figure from the legitimate dinasty. That said, certainly calling the comuneros revolt a democratic revolt is going too far, and as always things are more polifaceted than reductionist, teleologic interpreetations. We are in the early 16th century, in the alte 18th century and the 19th century getting rid of the monarch was still a challenge on the field of public mentalities and politically puzzling)
As I say, there was, for example, also vindication of old laws. The problem here is that we tend to understand history and specially Modernity as a continious linear path, thus the problems of interpretation with the Comuneros and with many other mevements around the Atlantic World in the Modern Age. To sumamrize, there is the possibility that medieval castilian laws and structures were closer to the liberal spirit than the alternative impossed by the Habsburgs, while at the same time they were the product of a feudal, or feudal-ish world.
That said, probably the key for a possible victory of the Comuneros, as far as I can think the only one, is in the meeting between Padilla and Juana in Tordesillas with a different result. A big problem for the Comuneros was that, despite they represented a larger portion of the castilian society than their foes, they weren't a match for nobiliar armies on the field. Their main forces, the Milicias Concejiles, were only partial-time light infantrymen designed as auxiliars in the battle and as public order force in peacetime so, we need a way to balance things. I think that it's possible to have Juana to sign the documents presented to her by the Santa Junta. Thus, as Adrian of Utrech feared in a letter sent to Charles ("if your mother joins the revolt the kingdom is lost", said) some important loyalties cound switch. Juana was sympathetic towards comuneros demands, and he had very kind words to Padilla ("go ahead, captain, and punish the bad guys" it's said she told him) but she didn't dare to take the risk of making their support official. Perhaps se still thought she had something to lose, perhaps it was a caprice or who knows. But a differetn outcome with the queen on a different mood is not totally out of possibility, also, some astute counterfaction of their sign could have made the work, but probably nobody thought on it.
So, if Juana joins the comuneros open and officaly some important players could start to rethink ther positions. I'm mainly thinking in the powerful Mendoza familly, also a familly known by their humanists, artistic patronage and some eccentrities. Padilla's wife, María Pacheco (who continued the combat from Toledo after her husband's death), not less, was a member of that familly. With the queen on the side of the Comuneros I think the Mendozas, or a part of them, could try some kind of William of Orange avant la lettre. They could add true soldiers to the Comunero army and attract to the cause smaller houses while other big famillies could start to evaluate their options and risks. In fact, some of th Mendoza, beyond María Pacheco, were symapthetic towards the comuneros in OTL, so I'm rather thinking on boosting and spreading this attitude.
Of course it could cause some problems regarding the form of the new state once there are big aristocrats involved, specially considering that in some parts of the crown the peasants had started to evict the nobles from their lands, but with a point of gravitation (the crown) and good results in the battlefield I think a compromise would be still possible. Still there would be probably a very clear political divide between the lands north of the Cantabric Range line and the lands in the plateau.
Finally, regarding Aragon, I think the most probable outcome is the disolution of the dynastic union, probably a friendly dissolution, since neither the castilian and aragonese Cortes were ever very enthusiastic with it. It's difficult to make the aragonese Cortes to officially proclaim a queen. Meanwhile, in the kingdoms of Valencia and Balearics a somewaht similar revolt to those of tha Comuneros is ongoing, and probably the Aragonese nobility would be as a quickly as possible to smash it after a different outcome right next door.
EDIT: I forgot. Regarding the aragonese question, probably we could have an interesting time after Juana's death in both iberian crowns and the inheritance.
Cheers.
