One of my very first alternate timeline ideas after joining this site was a timeline where Mary of Burgundy survived, and this is a much updated version of the Habsburg lineage for that TL.
Maximilian I, Holy Roman Emperor (b. 1459, d. 1519) m. Mary of Burgundy (b. 1457, d. 1514) in 1477, had issue (a);
1) Philip, Duke of Burgundy (b. 1478, d. 1512) m. Anne of York (b. 1475, d. 1510) [1] in 1494, had issue (a); Elisabeth Jagiellonica (b. 1482, d. ?) in 1512, had no issue (b)
1a) Charles, Count of Charolais (b. 1498, d. 1502)
2) Margaret, Duchess of Burgundy (b. 1480) m. Philibert II, Duke of Savoy (b. 1480, d. ?) in 1497 [2], had issue
1) Charles V, Holy Roman Emperor (b. 1499, d. ?) m. Elisabeth of Hungary and Bohemia (b. 1503, d. ?) in 1522, had issue
2) Francis (b. and d. 1501)
3) Margaret (b. 1503, d. ?) m. Louis II Jagiellon, King of Hungary and Bohemia (b. 1504, d. ?) in 1522 [3], had issue
4) Maria (b. 1504, d. ?) [4]
5) Stillborn daughter (b. and d. 1506)
3) Francis (b. and d. 1481)
4) Charles (b. 1483, d. 1485)
5) Eleanor, Queen of Spain (b. 1485, d. ?) m. Ferdinand VI, King of Spain (b. 1485, d. 1536) [5] in 1501, had issue
1) Juan III, King of Spain (b. 1503, d. ?) m. Isabella I, Queen of Naples (b. 1502, d. ?) [6] in 1521, had issue
2) Maria, Queen of Portugal (b. 1504, d. ?) m. João III, King of Portugal (b. 1496, d. ?) [7] in 1521, had issue
3) Fernando, Duke of Béjar and Plasencia (b. 1507, d. ?) m. Teresa de Zúñiga y Manrique de Lara, 3rd Duchess of Béjar and Plasencia (b. 1502, d. ?) in 1525, had issue
4) Alfonso, Cardinal and Archbishop of Zaragoza (b. 1509, d. ?)
5) Isabel (b. and d. 1512)
6) Pedro (b. and d. 1515)
6) Isabella (b. 1486, d. 1501) [8]
7) Anna, Queen of Poland and Grand Duchess of Lithuania (b. 1489, d. 1514) m. Sigismund I Jagiellon, King of Poland and Grand Duke of Lithuania (b. 1467, d. ?) in 1505, had issue
1) Sigismund Jagiellon, Crown Prince of Poland (b. 1510, d. 1511)
2) Alexander Jagiellon (b. and d. 1511)
3) Hedwig Jagiellonica (b. 1513, d. ?) m. ? [9]
4) Sophia Jagiellonica (b. and d. 1514)
8) Catherine (b. 1492, d. 1493)
[1] The Yorks remain on the English throne due to Elizabeth of York's betrothal to Charles VIII of France remaining in place after 1482.
[2] I couldn't resist giving Burgundy to Margaret and marrying her to Philibert ITTL. Also, Charles I of Savoy dies childless in 1486 so Philip II succeeds to Savoy much earlier than IOTL.
[3] Elisabeth and Louis are children of Vladislaus II and his ATL wife Elisabeth of the Palatinate.
[4] Maria enters a convent at a young age, as part of a promise that her father made to his dying mother.
[5] Catherine of Aragon is born male ITTL.
[6] Daughter of a surviving Ferdinand II, King of Naples and Maria of Aragon and Castile. She is the only child of her parents, as her father dies just a few months after her birth.
[7] Afonso, Prince of Portugal survives ITTL to become Afonso VI of Portugal and João is his eldest surviving son by Isabel of Aragon and Castile.
[8] Isabella of Austria-Burgundy was engaged to Vladislaus II at the time of her death so Max had to come up with a replacement real quick (he tried Anna at first but she was only 12 and thus way too young for Vladislaus).
[9] I'm not sure who this Hedwig Jagiellonica would marry...suggestions are welcome!