Neither Wilhelm nor Phil would be her choice (or her father's), since both require the political situation to be identical to OTL. Wilhelm was more interested in marrying first Kristina/Dorothea of Denmark (daughters of Christian II), then when thwarted there, he married Jeanne of Navarre. Then when that marriage was set aside, he married an Austrian archduchess. All of which benefitted him in some way. In the 1530s. Kristina/Dorothea as heiresses to the "spotty rich kid with a cool car" that was Julich, Jeanne because it got him French backing against Karl V, hjis Habsburg wife because it made peace with Karl over Guelders. Until Anne of Cleves married into England, England has no "pull" on Imperial affairs.
Phil's not gonna marry her for the same reason.
Neither Henry nor Anne is going to let her marry outside of England. @desmirelle pointed out once that Anne should've sent Mary to Scotland wrapped in a bow. Not because James wasn't going to invade but rather to "buy him off". James is a royal, and so long as his mom is alive, he's unlikely to invade (not to mention, his dad did that and look what happened). He's Catholic. Scotland isn't overly powerful and it's allied with Anne's great love: France. Karl V can't object because while he might have wanted Mary for his brother-in-law, the duque de Beja (he planned to make them duke and duchess of Milan and his "viceroys" in Italy), he can't deny the opportunity of getting Scotland to ditch the Auld Alliance for a shiny new imperial one.
Will Karl try to get James to invade? Unlikely. Since at Anne's execution in 1536, Elizabeth was betrothed to Felipe II. Karl V was a pragmatist. He made peace with Henry astonishingly quickly after Katherine of Aragon's death. He told his ambassador to inform Mary that "the emperor will not go to war for you" (or essentially, I'm not getting involved). With a son for Henry-Anne (i.e. vindication), Mary's in a much tighter spot by 1536 than she was OTL. Her options are submit or get locked up as a traitor.
See @Space Oddity's TL Now Blooms the Tudor Rose for ideas
Marrying James V to Mary seems very "match to powder keg" to me, personally. I just can't see hardcore Catholic James, with a deep dislike for the English, marrying Henry's daughter from his 'legal' Catholic marriage and agreeing to just hang out up North while Henry 'marries' the Protestant Anne and raises Protestant heirs with her...
Maybe if Francis I found a way to really screw Scotland over, and Karl V was pushing for the match with James, and there were literally no French matches to be found. There would have to be some kind of concession regarding Mary's rights, I think. Maybe Henry and James could agree to her children being in line to the throne after any brothers she may have, as well as their issue both male and female? Anne would be pissed, of course
I did not know that Elizabeth and Philip II were engaged in 1536 - I've never read anything about it. I always thought Anne wanted a French marriage for her... if Elizabeth was engaged to Philip II, I can see Henry and Karl finding a marriage for Mary at the same time. Maybe the Duke of Beja thing could work out after all - maybe he and Mary would both have to sign away any claims to England, and swear to never pursue their claims?
Let's say the first son is born in 1534, the second in 1535 or 1536, and the third some years after that (if at all).Anne tried to marry Mary to her cousin, the earl of Surrey, but later changed her mind and persuaded Henry to let Surrey marry Frances de Vere. There was also talk in the early 1540s of Mary's marriage ot Karl V taking place or Henri II's marriage being set aside (due to childlessness), neither happened.
The question of when the son is born is important. After Henry's 1536 jousting accident, he can't have said to have been the most stable of people. He flew into a temper when Karl V refused the remarriage option and suggested his brother-in-law, the duque de Beja (IIRC), and felt the French had been playing with him when Henri II's annulment wasn't granted. If there's a duke of York born a year/eighteen months after Anne's son, maybe a duke of Gloucester/Somerset after that, by 1540, Mary staying unmarried looks odd