It would be interesting if possible - John of Austria comes across as marginally more competent than the rest of the Spanish Hapsburgs. But the thing is, there were so many of them that were legitimate and could get together some support. And then there's the Austrian Hapsburgs.
Maybe Charles V, being the Emperor, creates a kingdom for John of Austria somewhere in Germany - that certainly is not going to happen in Spain, but somewhere in the Empire might happen. I'm not sure if that can "legitimize" him enough that, if enough legitimate candidates die prematurely, he might be picked as King of Spain.