Ok so, I've been mulling over this scenario, and while I was happy with what I said, I do have some new thoughts I want to discuss. For simplicity's sake, I'm going to call the children of Franz "of Austria", and the children of Philip "of Burgundy". It's easier than distinguishing the difference every time, particularly for my first point.
- I do not think Mary of Austria is going to marry into Portugal. Simply put, while Philip's line is going to be much more focused on Spain and it's neighbours, if Franz is going to be Holy Roman Emperor, his focus is going to be much more likely to land on neighbouring kingdoms like Hungary. So I propose that, along with Maximilian's marriage to Anne of Bohemia and Hungary, we have Mary marry Louis of Hungary as her cousin did OTL, leaving Mary of Burgundy free to either replace Eleanor of Austria as John III of Portugal's bride, or to marry someone important to her brother's political plans, like Charles III, Duke of Savoy. If that marriage happens, I could easily see Beatrice of Portugal becoming the wife of Ferdinand of Burgundy (who, in a funny turn of events, actually might be put forward as a replacement for Charles as Mary Tudor Jnr's husband), perhaps along with a greater focus on taking Milan and giving that Duchy to Charles' younger brother. As for Mary of Austria, I can see her marrying a second time more readily than Mary of Burgundy did OTL, because she'll have her father to pressure her into that decision. As for who, I would suggest either a widower Charles VIII, King of England, as it's been states he's living until his 60's. That might occur as part of the full separation between the Austro-Hungarian Hapsburgs and the Spanish-Hapsburgs. However, if that happens, it's likely Christine of Austria isn't going to marry Charles VIII's son, which leads me to my next point.
- Christina of Austria's marriage to a son of Charles VIII is great in theory, but I feel like we're missing a great opportunity for Franz to spread his influence elsewhere, via a marriage into the British isles. Now I'm not saying she should marry Henry VIII, King of England, because that's just cruel on what I imagine is a sweet young woman. But unless this timeline also involves a son being born between Henry VIII and Catherine of Aragon, and thus Mary Tudor marrying James V, King of Scotland, then there's suddenly the potential for a match between those two, particularly if France has no Princesses of the right age (probably too old). It gives James a marriage to the daughter of the Holy Roman Emperor, who is likely allied with the King of France, who is himself Scotland's ally under the Auld Alliance. It's honestly a strong match for Christina. Again, it depends on how the timeline goes and if Charles VIII has a son the right age, but that could lead to family drama for the Hapsburgs, particularly if they end up keeping Ferdinand from holding Milan.
- Now let's talk Margaret of Austria. OTL she was pretty much left off the hook after Philibert of Savoy died, but let's put that in perspective. Within two years of her second widowhood, her only brother/sibling was dead and her nephew needed a Regent. Here, not only is that covered by her other brother, but Maximilian has another son, which may decrease his sentimentality. While I doubt she'll be forced into a third marriage immediately, there's too much to be gained via her marrying again, particularly since she is so young. But she's not going to be considered a prime match by some. Two marriages that produced only one stillborn daughter is a bad look, but she's still young, beautiful and the daughter of the Holy Roman Emperor. Depending on how this goes, I could see her as the second wife of either Henry VII, King of England or Louis, Duke of Orleans. Orleans is a better match in terms of likelihood, considering her did marry again OTL, while Henry didn't. But that being said, the King of England did negotiate for her hand at one point OTL, only to turn and say he wanted Joanna, Queen of Castile instead. Maybe with Margaret being pushed into acceptance sooner, Henry VII actually ends up with a second wife. I will, for these family trees, go with the more likely Louis, but both men are entirely possible as her third husband. For the sake of the family trees, I'll show her children, and who they might be married to, in my best guesses based off this potential timeline. I'm going off the idea of a son and a daughter, born in 1509 and 1514. For the daughter (b.1509) she's probably going to marry into a French noble family. My first thought was the Guise family, but she'd be about 10 years Francis I, Duke of Guise's elder, so he's probably not going to happen unless it's a love match against everyone's expectations, after a first short marriage for her. This also cuts out the 8 years her younger Francis I, Duke of Lorraine (sorry, it's not my fault that all these men had the same name). However, Louis de Bourbon, Duke of Montpensier is about the right age (4 years her junior but that's workable) and he's a Prince of the Blood, which will work. As for the son, as of 1514, there's always the Lorraine and Guise families to look at again. Marie of Guise is actually the perfect age for him, as are most of her sisters. Anna of Lorraine is about 8 years younger, but a younger wife isn't something to really worry about and she's of a good family, but for this, I'd be more likely to go for Marie of Guise. Her age and family background is just too perfect for this.
Franz of Austria,
Holy Roman Emperor (b.1481: c.1532) m. Elizabeth of Austria (b.1485: d.1555) (a)
1a) Maximilian, Holy Roman Emperor (b.1502) m. Anne I, Queen of Bohemia and Hungary (b.1503) (a)
2a) Mary of Austria (b.1505) m. Louis II, King of Bohemia and Hungary (b.1506: d.1526) (a), Charles VIII, King of France (b.1470: c.1535) (b)
3a) Francis of Austria (b.1507) m. Anne Bathory (c.1530) (a)
4a) Christina of Austria (b.1510) m. James V, King of Scotland (b.1512) (a)
5a) Leopold of Austria, Archbishop of *Insert Name Here* (b.1512)
6a) Elisabeth of Austria (b.1515) m. Frederick III, Elector Palpatine (b.1515: d.1576) (a)
Philip IV,
Duke of Burgundy (b.1478: d.1506) m. Juana I,
Queen of Portugal (b.1479: d.1555) (a)
1a) Eleanor of Burgundy (b.1498: d.1558) m. Manuel I, King of Portugal (b.1469: d.1521) (a)
2a) Carlos I, King of Spain (b.1550: d.1558) m. Isabella, Princess of Portugal (b.1503) (a)
3a) Isabella of Burgundy (b.1501: d.1526) m. Christian II, King of Denmark (b.1481: d.1559) (a)
4a) Ferdinand, Duke of Milan (b.1503: d.1564) m. Beatrice of Portugal (b.1504) (a)
5a) Mary of Burgundy (b.1505: d.1558) m. Charles III, Duke of Savoy (b.1486: d.1553) (a)
6a) Catherine of Burgundy (b.1507: d.1578) m. John III, King of Portugal (b.1502: d.1557) (a)
Margaret of Austria (b.1480: d.1530) m. Juan,
Prince of Asturias and Girona (b.1478: d.1497) (a), Philibert II,
Duke of Savoy (b.1480: d.1504) (b), LouisI,
Duke of Orleans (b.1462: d.1515) (c)
1a) Stillborn Daughter (c.1498)
2c) Stillborn Son (c.1507)
3c) Marie d'Orleans (b.1509) m. Louis, Duke of Montpensier (b.1513: d.1582) (a)
4c) Charles II, Duke of Orleans (b.1511: d.1519)
5c) Miscarriage (c.1512)
6c) John I, Duke of Orleans (b.1514) m. Marie of Guise (b.1515: d.1560) (a)