One timeline I see being possible is:
1478: Philip of Austria is born.
1480: His sister, Margaret of Austria, is born.
1482: Philip of Austria succeeds his mother to the Duchy of Burgundy.
1494: Philip, Duke of Burgundy, takes control of his lands.
1496: Marries Joanna of Castile and Aragon.
1497: Margaret of Austria marries John, Prince of Asturias, who dies 6 months later and leaves behind a stillborn daughter and a young widow.
1498: Eleanor of Austria is born. Miguel de Paz is born.
1500: Charles of Austria is born. Miguel de Paz dies.
1501: Margaret of Austria marries Philibert II, Duke of Savoy. Isabella of Austria is born.
1502: Philip, Duke of Burgundy and Joanna of Castile and Aragon receive fealty as the heirs to Castile.
1503: Ferdinand of Austria is born.
1504: Philibert II, Duke of Savoy dies. Margaret of Austria is a widow again. Isabella I of Castile dies. Joanna of Castile and Aragon becomes Joanna I of Castile.
1505: Mary of Austria is born.
1506: Philip and Joanna become stranded in England and to be allowed to leave, Philip signs a treaty entitles Malus Intercursus, which makes him send any English rebels he has back to England. When the couple eventually arrives in Corunna, Philip and Ferdinand II of Aragon argue and eventually come to an agreement, which ends in the Treaty of Villafafila. Philip is crowned Philip I of Castile. He is struck by Typhoid fever but recovers.
1507: Catherine of Austria is born. Margaret of Austria is married to Christian of Denmark.
1508: Maximilian of Austria is born.
1509: Henry VII of England dies and his son Henry, Prince of Wales succeeds him as Henry VIII of England.
1510: John of Denmark is born.
1511: Anne of Austria is born.
1512: Barbara of Austria is born.
1513: Christian of Denmark becomes Christian II of Denmark.
1514: Louis XII of France dies. Margaret of Austria dies giving birth to Christina of Denmark. Christian II of Denmark morganically marries Dyveke Sigbritsdatter. Frederick of Austria, the last child of Joanna I of Castile and Philip I of Castile, is born. He dies later that year.
1515: Mary of Austria marries Louis II of Hungary.
1516: Charles of Austria marries Anne of Bohemia and Hungary. Mary Tudor is born. Ferdinand II of Aragon dies. Philip and Joanna of Castile take the throne. Barbara of Austria dies.
1517: Isabella of Austria marries Charles III, Duke of Savoy. Philip I of Castile discovers his daughter Eleanor has started a relationship with Frederick von Wittelsbach. He hurries her marriage to John, Crown Prince of Portugal.
1518: Dyveke Sigbritsdatter dies giving birth to Christian II of Denmark's third child, a stillborn daughter. Later in the year Ferdinand of Austria marries Anna of Cleves, 8 years older than him.
1519: Maximilian, Holy Roman Emperor dies. Philip I of Castile becomes Holy Roman Emperor.
1520: Philip I of Castile announces to his children how he plans to carve up his empire when he's gone, due to the feeling of old he has at 42. Charles will get burgundy and the Holy Roman Empire. Ferdinand will get Spain. And finally, Maximilian will get Austria.
1522: Mary of Austria receives her coronation and becomes Queen of Hungary.
1524: Catherine of Austria marries James V of Scotland.
1525: Henry VIII begins the process of having his marriage to Catherine of Aragon annulled. Philip I of Castile opposes.
1526: Louis II of Hungary dies in the Ottoman invasion, leaving Charles of Austria and Anne of Bohemia and Hungary as rulers. In lieu of any other options, Philip I of Castile sends word that Mary must remain as a regent.
1528: Philip I of Castile and Henry VIII of England come to an agreement. Philip will support the annulment of the English King's marriage, if he will marry Anne of Austria and have his daughter Mary married to Maximilian of Austria.
1530: Anne Boleyn leaves the court after the marriage of Henry VIII of England to Anne of Austria. She will later and take her place as his mistress in 1532.
1537: Philip I of Castile dies, leaving his eldest son to become Charles, Holy Roman Emperor, his middle son as Ferdinand of Spain and Maximilian as Archduke of Austria and possible future King of England.
Maximilian I, Holy Roman Emperor (b.1459: d.1519) m. Mary of Burgundy (b.1457: d.1482), Anne of Brittany (b.1477: d.1514) -annulled 1490-, Bianca Maria Sforza (b.1472: d.1510)
1a) Philip the Handsome, I of Castile and Aragon, Duke of Burgundy and Holy Roman Emperor (b.1478: d.1537) m. Joanna I of Castile and Aragon (b.1479: d.1555)
1a) Eleanor of Austria (b.1498: d.1558) m. John III of Portugal (b.1502: d.1557) (a)
1a) John of Portugal (b.1520)
2a) Maria of Portugal (b.1521)
3a) Eleanor of Portugal (b.1524: d.1526)
4a) Luis of Portugal (b.1526: d.1530)
5a) Isabella of Portugal (b.1527)
6a) Beatrice of Portugal (b.1530: d.1531)
2a) Charles V, Duke of Burgundy and Holy Roman Emperor (b.1500: d.1558) m. Anne of Bohemia and Hungary (b.1503: d.1547) (a)
1a) Philip of Austria (b.1518)
2a) Mary of Austria (b.1519)
3a) Margaret of Austria (b.1520: d.1530)
4a) Charles of Austria (b.1522)
5a) Anna of Austria (b.1525)
6a) John of Austria (b.1527: d.1530)
7a) Catherine of Austria (b.1529: d.1529)
8a) Barbara of Austria (b.1532)
9a) Elisabeth of Austria (b.1535: d.1541)
10a) Helena of Austria (b.1536)
11a) Maximilian of Austria (b.1538: d.1540)
12a) Ferdinand of Austria (b.1540)
13a) Magdalena of Austria (b.1544)
3a) Isabella of Austria (b.1501: d.1532) m. Charles III of Savoy (b.1486: d.1553) (a)
1a) Louis of Savoy (b.1520: d.1523)
2a) Beatrice of Savoy (b.1521)
3a) Emmanuel of Savoy (b.1523)
4a) Charles of Savoy (b.1525)
5a) Isabelle of Savoy (b.1527: d.1528)
6a) Christine of Savoy (b.1527)
7a) Philibert of Savoy (b.1528: d.1533)
4a) Ferdinand V of Castile and III of Aragon (b.1503: d.1564) m. Anna of Cleves (b.1495: d.1521) (a), Isabella of Portugal (b.1503: d.1539) (b), Margaret de Valois (b.1523: d.1574) (c)
1a) Mary of Austria (b.1519: d.1520)
2b) Philip of Austria (b.1523)
3a) Isabella of Austria (b.1524: d.1527)
4a) Martin of Austria (b.1525: d.1525)
5a) Ferdinand of Austria (b.1530)
6a) Maria of Austria (b.1533)
7a) John of Austria (b.1534: d.1534)
8a) Constance of Austria (b.1536)
9c) Claudia of Austria (b.1544)
10c) Charles of Austria (b.1550)
11c) Elizabeth of Austria (b.1555)
5a) Mary of Austria (b.1505: d.1558) m. Louis II of Hungary (b.1506: d.1526) (a)
6a) Catherine of Austria (b.1507: d.1578) m. James V of Scotland (b.1512: d.1542) (a)
1a) James VI of Scotland (b.1528)
2a) Alexander Stewart (b.1530: d.1530)
3a) Margaret Stewart (b.1532)
4a) Stillborn Boy (c.1533)
5a) Mary Stewart (b.1535: d.1539)
6a) David Stewart (b.1538: d.1539)
7a) Stillborn Boy (c.1539)
7a) Maximilian, Archduke of Austria (b.1508: d.1560) m. Mary Tudor of England (b.1516: d.1558) (a)
1a) Henry X of England (b.1529)
2a) Stillborn Boy (c.1532)
3a) Miscarriage (c.1535)
8a) Anne of Austria (b.1511: d.1559) m. Henry VIII of England (b.1491: d.1545) (a)
1a) Elizabeth Tudor (b.1530: d.1543)
2a) Edward VI of England (b.1533: d.1546)
3a) Miscarriage (c.1534)
5a) Margaret Tudor (b.1536)
6a) Henry IX of England (b.1539: d.1550)
7a) Stillborn Girl (c.1542)
9a) Barbara of Austria (b.1512: d.1516)
10a) Frederick of Austria (b.1514: d.1514)
2a) Margaret of Austria (b.1480: d.1514) m. Juan, Prince of Asturias (b.1478: d.1497) (a), Philibert II, Duke of Savoy (b.1480: d.1504) (b), Christian II of Denmark (b.1481: d.1559) (c)
1a) Stillborn Girl (c.1498)
2a) John II of Denmark (b.1511: 1578) m. Amalia of Cleves (b.1517: d.1586) (a)
1a) Dorothea of Denmark (b.1540)
2a) Christian of Denmark (b.1544)
3a) Christina of Denmark (b.1514: d.1562) m. Francesco II Sforza, Duke of Milan (b.1495: d.1535) (a)
1a) Francesco III Sforza, Duke of Milan (b.1531)
2a) Catharina Sforza (b.1532: d.1532)
3a) Isabella Sforza (b.1533: d.1534)
4a) Maria Claudia Sforza (b.1534)
5a) Ludovico Sforza (b.1535: d.1535)
6a) Bianca Sforza (b.1536: d.1538)