All the advice given to Mary at this period from the Imperial Ambassador and her own domestic supporters was 1) To submit to her father in terms of the supremacy and 2) to not leave the country.
To flee would have placed her at the head of any future foreign invasion and most recognised that whilst there was considerable domestic sympathy and support it would be significantly erroded if she was seen as the puppet of a foreign power.
Actually that is very much wrong. That advise only came AFTER Anne Boleyn's execution, once it became obvious that the King had no intention of restoring Mary to her previous position. Before that Mary and Catherine's supporters seriously entertained the idea of getting them out of the country.
And I think your vastly underestimating the real situation in England at this point. The King's popularity was at its lowest point, while Catherine and Mary were regarded by many as living saints. Mary fleeing would create a difficult situation for all, as she is the rightful heiress of England in the eyes of the Catholic world. And I'm sure she would make some kind of proclamation saying that she is forever loyal to her father but fears for her life because of Anne Boleyn. It would gain her more sympathy in England while further degrading her father's popularity and reputation abroad.
Mary would be the obvious choice to act as a figurehead for any invasion yes, but there's also a big chance that dissatisfied nobles will reach out and offer to rise if an invasion was to occur. Considering the King's unpopularity and favoritism of Boleyn's family and new men, I think the more established nobles will take advantage to regain lost power and side with Mary.
agreed, Mary leaving was the last resort only to be undertaken if her life was in danger, as often people believed it was from Anne, but yes, the English were not ready or willing to support a foreign invasion no matter who was its titular head
whatever interesting PODs that Mary leaving England sets off, a Spanish conquest of England in the name of the Catholic Church isn't one of them
I would be interested to see if her leaving would lead to changes with Henry FitzRoy
Again your wrong. The fact that many nobles reached out to the Emperor during 1534-36 offering to rise in favor of the Princess if Charles invades shows the real situation behind the scenes. Mary would be a convenient figurehead not only for a potential invasion but also for dissatisfied nobles who are angry at the King and his advisers.
And with Mary in Brussels and the Pope saying she's the rightful Queen, I feel that the Emperor would be paraded into action.
Wasn't he part of the church at this point?
OK couple of things. One, you might want to create a separate thread for the actual TL, it makes it easier to read. Second, the Empress Isabella never left Spain, as she was Regent for her husband there during his frequent absences. Mary of Austria, Queen Dowager of Hungary was the Governor of the Netherlands at this point. Third, Henry VIII isn't that likely to actually put Catherine on trial, much less execute her. It doesn't matter what his ego was, this would make England a pariah state and Henry (or his advisers) would know this. It would permanently end any chance of an alliance with the Emperor.
As to marriages, the best choice at this point would be King James V of Scotland, Mary's first cousin. The chance to be jure uxoris King of England might be enough to have James drift from an alliance with France to one with the Emperor. Other options would be Henri de France, Duc d'Orleans (unlikely but possible), Louis, Duke of Beja, and maybe John of Denmark (son of deposed King Christian of Denmark and the late Isabella of Austria) if you want to have him survive.
As to Reginald Pole, yes and no. He as a Cardinal but never took holy orders, so he would be a (very) unlikely option. I doubt Pole was ever seriously considered as a bridegroom for the Princess.