I do believe that akhenaten was Tut's father but to play devils advocate, if the was indeed a co-regency between Akhenaten and his father, and lets say for a second that it was a long one, about 12 years. If Tut was fathered during the last few years of the co-regency and then Akhenaten reign for a further 5 years on his own (he reigned for about 17 years in total) Tut could be Amenhotep's father, maybe by one of his daughters or even Tiy.

DIDNT ONE OFF TUT'S DAUGHTERS DIE AT 7 MONTHS PREGNANCY, AND THE SECOND ONE SHORTLY AFTER BIRTH?????

AND NEFERTITI AS HIS FATHER NOW THAT IS BREAKING NEWS THE VERY FIRST TIME A WOMAN IS FATHER OFF THE CHILD

"That's not a lady, that's a man!" lol, sorry, random inside joke.

Anyways, I don't think Tut could be Tiye's son. Possibly one by Amenhotep and a minor wife/daugher, but Tiye would've been around 30 or 40, and a bit too old to be having children.

Although Maya was the name of Tutankhamen's treasurer, there are two women who had the same name. One was a wet-nurse for the infant Tutankhamen, and there has been specultion that she may have been Tut's mother.
Kiya has been ruled out, mainly because all existing records state that she had only one child--a daughter.
I think the Amenhotep III co-regency is more than possible. All the evidence for it is in the book by Fredrick Giles--"The Amarna Age--Egypt". It is an excellent book! Be sure to get Egypt--it comes in several versions. His theories of the co-regency convinced me.