In 1664 the following Habsburg males (legitimate, not major power rulers, so Leopold I is not counted) were alive:
http://en.wikipedia.org/wiki/Karl_Josef_of_Austria
http://en.wikipedia.org/wiki/Archduke_Sigismund_Francis_of_Austria
After their death Leopold I was pretty much left the only living healthy adult Habsburg male in ALL branches.
And there were no cadet legitimate branches, and only Juan Jose as known illegitimate male (obviously not a consort for Margaret Theresa as he's her half-brother and not even Habsburgs were into THIS).
Margaret Theresa would be of perfect age for Karl Josef. Sigismund Francis is a bit too old, but he proved himself a capable ruler back in Tyrol and will push both Queen Regent and Juan Jose away from ruling once he becomes Consort of Spain.
Perfect compromise candidate for 1664-1667 is Charles V of Lorraine. As unlike say 1674, France has literally no one to be offered as Prince Consort - all Bourbon Princes of Blood at this point are either married or have their age in single digits.
Karl Josef would be the best bet, and I guess Sigismund would also be considered (the Tyrol would either be in personal union with Spain or turned over to the Emperor).
Yeah I think everyone forgets that Juan Jose is her BROTHER, so no way that the Pope would grant a dispensation for that (a little to Egyptian). Not to mention the Queen Regent seemed to hate him and I can't see her marrying her only surviving child off to Don Juan even if it was viable.
And Duke Charles V would be a good candidate, he's a Habsburg hanger on and wouldn't have any lands to place in union. Though I can't help but wonder if he would try to use Spanish resources to attempt to regain the Duchy of Lorraine.