If Charles V remarries, I doubt it would be one of his nieces. Despite all the inbreeding amongst the Habsburgs, the first uncle-niece marriage in the family wasn't until Philip II married Anna of Austria in 1570--and that took a great deal of maneuvering on his part to secure the dispensation from Pope Pius V, who was never fully comfortable with doing so. As far as Mary I of England is concerned, that wouldn't be possible until her accession in 1553. By that time, Charles V was an old man and, quite frankly, an exhausted one, hence the preference for Philip II in OTL.
Margaret is an interesting candidate. She was betrothed to Philip II, I believe as part of the Truce of Nice in 1538, but the precontract was later annulled after war broke out between France and the Emperor again four years later. This is a good window of time. Perhaps in this scenario, Charles V decides to wed Margaret himself, seeing as she's four years Philip's senior and already of age at this point (he'll probably still go through with a match with the Avis for his son as in OTL). I can't see this changing the diplomatic situation of OTL much, though. The truce will still most likely fail.
Alternatively (and perhaps more realistically), you could also have Charles wed her as part of the settlement of the Treaty of Crépy (1544). By that time, Philip II is already married, so it would probably make a great more deal of sense. This means that François' son, the Duc d'Orléans, is still precontracted to Ferdinand I's daughter, Anna of Austria, and promised the Duchy of Milan, while, in this scenario, Charles then weds Margaret to cement the agreement.
Considering Margaret was in her late thirties when her OTL marriage took place, that may account for her low fertility. In this scenario, if she and Charles manage to produce a son (probably born ca. 1546-1550), he'll most likely be given the Low Countries. That is probably going to have HUGE consequences and many butterflies. Alas, I'm not well versed enough in the history of the Low Countries to offer much more than the following:
This hypothetical son, we'll call him 'Charles III of Burgundy', will be around only 8 to 12 years old when his father dies. If he's raised in the Netherlands, he won't be seen as a foreign ruler like Philip II was in OTL, and he'll also have far more of an understanding of his subjects there (read: a likely continuation of his father's policies). I can easily see the Estates insisting that the boy be brought up there and not in Spain. I'm not sure who his regent will be, perhaps Margaret of Parma? If so, she'll have far more of a free hand to dictate policy than Philip II gave her in OTL, and, in my opinion, that is definitely for the best, considering he and the Duke of Alva basically botched the job royally.
Amitiés,
Endymion