WI Anne of France was born a boy.

1. Duc de Bourbon likely gets married to (ATL Louis XII) sister Joan, as Louis XI is against Bourbon-Orleans alliance, and will stop the Duc's match to Marie d'Orleans.
2. The ATL Louis XII will be of right age to court Mary of Burgundy, and court he will by any means. Anne of Britanny may be reserved for a child from this union. Habsburgs get a short end of stick TTL.
3. OTL Charles VIII lives unremarkable life as Duc de Berry, maybe dies of something stupid TTL as well
 
Anne of France was the oldest child of Louis XI and Charlotte of savoy born in 1461. So WI the pregnancy that led to her birth produced a male, how would this effect things.

So just to make it easy for us to know who TTL Anne is I will name him Alexandre I.
Although he would most likely be named Louis (XII) or Charles (VIII)

So born on 3 April 1461, Dauphin Alexandre, is the eldest son of Louis XI of France and his second wife, Charlotte of Savoy.

Shortly after her birth, the king signed an agreement to marry her to his second cousin, Marie, the eldest daughter of Charles, Duke of Orléans, and his third wife Marie of Cleves.

He succeeds his father, Louis XI, when he died in August 1483, Alexandre I would also lose his mother, a few months later, and at twenty two, was King of France, with his sister, Joan and his thirteen year old brother, Charles as wards, he appointed their care to his Lord Chancellor, Baron François de Linières and his wife, Anne de Culan.

After 10 years on the throne, Alexandre, lost his first wife Marie, who had gave him, a daughter and son.
Two years later, he would marry 15 year old, Margaret of Austria, the second child and only daughter of Maximilian of Austria and Mary of Burgundy.
Margaret would spend the rest of Alexandre's reign by his side, until his death in 1522.

Alexandre, has wives A) Marie of Orleans (M.1476 D.1493) B) Margaret of Austria (M.1495 W.1522)
Children:
1a) Anne (1488)
2a) Charles (1489)
3b) Frances (1496)
4b) Still born girl (1498)
5b) Maria (1501)
6b) Henri (1505)
1b)
 
Here's my idea:

On the 3rd of April, 1461, the King of France finally was given a healthy Dauphin. Named John, this son would survive as the others had not and was followed by 4 more siblings, two of which (Charles, Duke of Berry and Joan of France) would also survive their infancy. And thus, the future John III of France was to begin. John la Grande, as he was known as a child, was quite intelligent and at the age of 9 presented his mother with a translation of the Gospel of John, showing his connection to John the Evangelist that stayed with him from his youth.

On the 18th of March, 1480, John la Grande watched his only sister Joan of France marry the Count of La Marche, future Duke de Bourbon. This marriage would remain childless and, when in 1495 the Duke de Bourbon applied to have his marriage annulled so that he might marry the Princess Anne of France, who was the child of John as the King of France.

As to the King's own marriage, in 1477 he rebelled against his father and married Yolande of Lorraine, after his father had gone out of his way to arrange a marriage between the Dauphin and Joanna la Beltraneja of Castille, who had fled to France in 1474 with the promise of a match between the two under her mother's guidance. Now without support, she returned to Castille in shame and on the last days of the year married her maternal uncle, King Afonso V of Portugal, giving him a single son in 1480, named Afonso.

With Yolande of Lorraine, John would have 8 children, of which 4 would survive: Anne of France (b.1482), Louis, Dauphin of France (b.1484), Francis, Duke of Anjou (b.1487) and Michelle of France (b.1492). Of these children, Anne would marry the Duke of Orleans in 1500, giving him 3 daughters and a son in the wake of his childless nature: Marie d'Orleans (b.1503), Claude d'Orleans (b.1509), Jacques d'Orleans (b.1510) and Renee d'Orleans (b.1513).

On the 1st of May, 1492, John III of France pushed and succeeded in finalizing the marriage between his younger brother and Margaret of Austria, after his first choice of Anne I, Duchess of Brittany ended with her married to the Holy Roman Emperor in 1490, and the couple had two sons: Arthur (b.1495) and Frederick (b.1499). With his bride Charles, Duke of Berry would have only one child, Marie de Berry (b.1498) before he died of a fever that same year. His bride would remarry to the Duke of Savoy, before retreating into a convent.

In 1485 John III supported Henry Tudor to the Kingdom of England, with the strict promise that Henry's eldest son would marry a daughter of the King of France. This wish came true in 1502, when Arthur Tudor married Michelle of France, the 10 year old Princess. Arthur would die young, aged 20, in 1506 and his widow, still physically a child and not having consummated the marriage, went on to marry his younger brother Edward, born 1488, the year after.

His son and heir would marry, in 1500, the Infanta Catalina (Catherine) of Aragon. The couple would undergo 9 recorded pregnancies, of which only 2 children survived: Charles VIII of France (b.1506) and Louise of France (b.1512). To add to this situation, the King's only brother Francis, Duke of Anjou suffered a great fall in 1511 and died, aged 24. This ended his betrothal to the Princess Mary Tudor.

Louis XI of France (b.1423: d.1483) m. Margaret Stewart of Scotland (b.1424: d.1445) (a), Charlotte of Savoy (b.1441: d.1483) (b)

1b) Louis, Dauphin of France (b.1458: d.1460)

2b) Joachim of France (b.1459: d.1459)

3b) Louise of France (b.1460: d.1460)

4b) John III of France (b.1461: d.1522) m. Yolande of Lorraine (b.1460: d.1510) (a)

1a) Joan of France (b.1479: d.1481)

2a) Anne of France (b.1482) m. Louis, Duke of Orleans (b.1462: d.1515)

1a) Louis d'Orleans, Count of Blois (b.1502: d.1505)

2a) Marie d'Orleans (b.1503)

3a) Miscarriage (c.1505)

4a) John d'Orleans, Count of Blois (b.1507: d.1508)

5a) Claude d'Orleans (b.1509)

6a) Jacques, Duke of Orleans (b.1510)

7a) Renee d'Orleans (b.1513)​

3a) Louis XII of France (b.1484: d.1540) m. Catherine of Aragon (b.1485: d.1536) (a)

1a) Louis, Dauphin of France (b.1504: d.1509)

2a) Charles VIII of France (b.1506)

3a) Miscarriage (c.1507)

4a) Louis of France (b.1508: d.1508)

5a) Francis of France (b.1510: d.1510)

6a) Louise of France (b.1512)

7a) Miscarriage (c.1513)

8a) John, Duke of Anjou (b.1515: d.1520)

9a) Miscarriage (c.1518)​

4a) Francis, Duke of Anjou (b.1487: d.1511)

5a) John of France (b.1490: d.1490)

6a) Michelle of France (b.1492: d.1518) m. Arthur Tudor, Prince of Wales (b.1486: d.1506) (a), Edward VI of England (b.1488: d.1543) (b)

1b) Margaret Tudor (b.1510)

2b) Isabelle Tudor (b.1512)

3b) Henry Tudor, Prince of Wales (b.1514)

4b) Mary Tudor (b.1515)

5a) John Tudor, Duke of York (b.1517)​

7a) Miscarriage (c.1493)

8b) Marguerite of France (b.1496: d.1497)​

5b) Joan of France (b.1464: d.1505) m. Peter II, Duke of Bourbon (b.1438: d.1503) (a)

6b) Louis of France (b.1466: d.1466)

7b) Charles, Duke of Berry (b.1470: d.1498) m. Margaret of Austria (b.1480: d.1530) (a)

1a) Louis, Duke of Berry (b.1497: d.1503)

2a) Marie de Berry (b.1498) m. Charles III, Duke of Bourbon (b.1490) (a)

1a) Marguerite de Bourbon (b.1517)

2a) Francis I, Duke de Bourbon (b.1519)

3a) John de Bourbon (b.1520)

4a) Anne de Bourbon (b.1522)

5a) Miscarriage (c.1523)

6a) Sophie de Bourbon (b.1525)​

8b) Francis of France (b.1472: d.1473)​
 
1. Duc de Bourbon likely gets married to (ATL Louis XII) sister Joan, as Louis XI is against Bourbon-Orleans alliance, and will stop the Duc's match to Marie d'Orleans.
2. The ATL Louis XII will be of right age to court Mary of Burgundy, and court he will by any means. Anne of Britanny may be reserved for a child from this union. Habsburgs get a short end of stick TTL.
3. OTL Charles VIII lives unremarkable life as Duc de Berry, maybe dies of something stupid TTL as well

I will go with this scenario.

Knowing Louis XI, only a miracle or a catastrophe will prevent his son to not marrying Mary of Burgundy (assuming that she will be the only heir of her father as OTL).
 
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Louis XI, but I agree. No way he'll have his son (John or Louis) to marry any no-name like Yolande of Lorraine (Louis XI did not obey his father's plans, but for political reasons - he married "as Dauphin, not as a king" to a princess from the long-standing ally of Dauphine region), when there is a greatest heiress of Europe on the mark. Even though she's 4 years older than the Dauphin.
 
Louis XI, but I agree. No way he'll have his son (John or Louis) to marry any no-name like Yolande of Lorraine (Louis XI did not obey his father's plans, but for political reasons - he married "as Dauphin, not as a king" to a princess from the long-standing ally of Dauphine region), when there is a greatest heiress of Europe on the mark. Even though she's 4 years older than the Dauphin.

I totally agree, Louis XI can call dibs at least before the treaty of Péronne. Before that, if not great, you can expect Charles the Bold to be at least civil and behave like a good vassal to his cousin. Afterwards, he's de facto independent. Keeping the treaty of Péronne, now matter how detrimental to the French King on the short-term, keeps Bourgogne in, and that's what matters most.
 
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