I'm pretty sure that Mutemwiya wasn't the premier Great Royal Wife. I'm almost positive that she wasn't given that status during her husband's reign and only really gained it when her son became pharaoh?
Tuthmosis IV had two other wives who played a role during his reign: Nefertiry and Iaret. Iaret was his sister, but seems to have come on the scene after year 5 if I remember correctly. Nefertiry's background is not known for as far as I know.
As for Nefertiti, if she was the niece of Tiy, as many suspect, then we don't have to look far for the one who would have promoted the match. I'm sure Tiy would have wanted to keep things in the family. Besides who were the other choices? Princess Baketaten would have been far too young:-)
I'm not sure I believe that Aye was her father. It seems to be based on his title of It Netjer (God's Father). There's really not much evidence for this theory.
Apparently the Vizier Aperel held this same title (It Netjer) as well as some others he had in common with Aye. Aperel's wife Taweret was buried with even more spectacular funerary equipment as Tuya, Queen Tiye's mother.
So I think it would be just as easy to argue that Aperel was Nefertiti's father.
Not that I would bet on him being the father either...
And Akhenaten had plenty of royal sisters: Sitamun, Iset, Henuttaneb, Nebetiah and Beketaten. Amenhotep III seems to have married Sitamun and Iset himself (kinda odd). But there were plenty of Royal princesses available it seems to me
I always found it interesting that Nefertiti's sister appears at court. You don't really see any other Queen's sisters in the history of AE (Can't think of any other examples). So why was the Queen's Sister Mutnodjemet present? Always made me wonder if they belonged to some collateral branch of the royal family. That's the only reason I can see for Princess Mutnodjemet to be present with the royals. But that's all guesswork on my part
Fun and interesting to think about, isn't it?