To whom will OTL Holy Roman Emperor Charles V be married ITTL? Also even if Charles wouldn't be elected Holy Roman Emperor, he would still be king of Castille, heir to the kingdom of Aragon etc., archduke of Austria, duke of Burgundy (and 'sovereign lord' of the Netherlands) etc.; in short a much better match than Edmund Tudor.
OTOH Isabella wasn't the first choice for a bride for OTL Charles V, Mary Tudor, the sister of Arthur Tudor and Henry VIII (due to the young of his (Henry VIII) daughter Mary, she never was a serious option, since Charles needed an heir and couldn't afford to wait) was .