A while back, I wrote an (unfinished) TL concerning this scenario. The title was "Jo El Rei", if you're interested in looking through the archives (someday perhaps I'll go back to writing it if I have time).
Both Razgriz and Falecius have the right idea. An independent Aragon under the Prince of Girona would undoubtably be pro-Habsburg, at least at the onset and mostly out of necessity.
First, you have strong family ties (technically Charles V is Juan's nephew), which at this time in European politics still means a great deal. As mentioned, there's also the issue of Aragon's interests in Italy, with the annexation of Naples in 1504. Curiously, Naples might not be as much of a sore point between France and Aragon in this scenario, as the treaty between Louis XII and Ferdinand II, signed at the time of the latter's marriage to Germaine de Foix, renounced the Valois claims to Naples and recognised the right of Ferdinand's children by Germaine to that kingdom (part of a brief compromise that was rendered moot in OTL). This not withstanding, French ambitions in Milan are counter to Aragonese interests for purely geopolitical reasons, and Juan will support the Sforzas and the Imperial faction at all costs against the Valois.
Apart from Italy, Aragonese foreign policy will also be highly concentrated on North Africa. It's important for Aragon to maintain its naval supremacy in the Medeterranian. In OTL the Turks were a constant headache, as they supported the Barbary Pirates who raided the coasts of Valencia and Catalonia, crippling commerce. At the very least, Juan will need to successfully capture Algiers and Tunis to maintain his goals. If the French still ally with the Ottomans as in OTL, this means an even stronger anti-French position in Aragon.
There's also the issue of Navarre. As mentioned, Ferdinand II will annex the kingdom for Aragon and not Castile in this scenario—for a variety of historical, geopolitical and dynastic reasons, the least of which being his wife's claims and Aragon's own past personal union with that realm. The Albrets will be supported by the Valois, which means even more reasons to ally with the Empire.
Aragon is also going to face a lot of internal problems in the early reign of Juan. The revolt of the Germanies will most likely occur on schedule (it was for different reasons than the Communeros in Castile). Catalan trade has also been damaged by piracy, as I've stated, though at least Valencia was showing signs of recovery. Most likely, Alonso d'Aragon, Juan's elderly, bastard half-brother and the Archbishop of Zaragoza, will be named as regent. If he still dies on schedule, several years later, than Germaine will probably be the next choice—and in OTL, she showed herself ruthless, pragmatic and competent in governing Valencia for Charles V and putting down the revolts there.
Above all, Juan is going to have a lot of work to do, and in order to do well as king, will need to be just as clever and duplicitous as his father. If he's smart, may entertain a French alliance from time to time for pragmatic reasons—such as avoiding the cost of war and keeping Charles V from becoming too imperious of an ally (no pun intended), but in the end, he's going to be pro-Habsburg.
Hope that helps.
Amitiés,
Endymion
Thanks, I am now back at this idea so you have helped tremendously. What about the Hapsburgs and their lands?