OKay Ankhesenamun 3, you have asked a couple of million dollar questions!
Many are the Egyptianologists that would pay to know what you are asking.

Joyce Tyldesley in her book Nefertiti writes on page 168-167.
The younger Meritaten and Ankhesenpaaten "appear to be the daughters of an unnamed king, who is generally assumed to be Akhenaten." She goes on " The clear implication is that Meritaten and Ankhesenpaaten must have been the mothers of their father's children." Oh boy! Isn't that convincing? Note the words... appear to be, generally assumed, clear implication, must have... if we used those words in a court of law we would be thrown out.
However, once again there is no proof of this... another reason why myself when discussing the Amarna Royals, i insist on knowning the "proof" of the stated belief. Because so many of the "beliefs" and "facts of knowledge" are based only upon speculation and little more. If the proof is substantial i accept it... if it is mostly circumstantial, or speculative i don't have to accept it. i am free to look at it more as an cultural anthropologist where the study of man within his culture is looked at. This allows me to try to come to a more reasonable explaination if there it one. Few Egyptianologists are anthropologists, most are simply archaeologists.
The standing belief regarding these royals. Is Meritaten married her father then gave birth. She then married Smenkhkara who had become co-regent and Akhenaten married Ankhesenpaaten who then gave birth to another daughter. Then when Akhenaten, Smenkhkara, and Meritaten died, Ankhesenpaaten married Tutankhamun.
What supports this belief is the fact that Amenhotep III did marry his daughters Sitamun, and Isis. (Some, myself included believe Sitamun to be his sister, adopted by him and his wife.) But Isis was Tiy's daughter by him. There is one other piece of support for this belief and it is the mention by the King of Babylon of Meritaten as "Misterss of your (Akhenaten) house".
The problems are:
1) The king is unnamed.
a. Akhenaten never had any problem with aknowledging the births of his
royal daughters by Nefertiti or by Kiya surely he wouldn't have had a
problem with aknowledging the daughters of his daughters if he was
the father.
b. Smenkhkara was also a king at Amarna and he was co-regent to
Akhenaten. As coregent in Akhetatan, had he fathered a daughter
while Akhenaten was alive would he let Smenkhkara be named?
2) It says the child is born of the King's daughter... it is assumed to be
Meritaten and Ankhesenpaaten. It could be Princess Beketaten,
a King's daughter and of childbirthing age was well. We do know that,
Beketaten visited late in the reign. Did she perhaps marry her
brother? Just who would have been a suitable husband for the
daughter of Amenhotep III and Tiy? She just disappears after that
visit was it into her brother's harem?
3) Now naming these daughters after living ones despite the experts who
want to see this as proof of their being born of, by the same named
women. It isn't proof.
a. Meketaten may very well be the mother of one of them. Naming her
child after her closet sister.
b. Let us assume that Meketaten wasn't the mother of one of them.
Akhenaten had a harem...not long after the death of Meketaten,
Nefertiti, Queen Tiy, and Kiya disappear. Suddenly, the number one
women in court are Meritaten and Ankhesenpaaten. Bekeataten, or
an even lower women of the harem might have named the children
after the new primary women of the court.
4) Smenkhkara was apparently an adult when he became co-regent.
Egyptians married young. While Akhenaten married daughter after
daughter, having more daughters Smenkhkara just waited with lower
ranked women?
5) If the younger Meketaten was capable of having a child, why wasn't her
older sister?
6) The marrying of one's daughter while not abnormal in Egyptian royal
history/culture happened rarely. However, the marrying of a daughter
then passing her on to your successor is, and is not recorded anywhere
in Egyptian history. Which is the favored theory of archaeologists where
it would send grave warning signals to anthropologists
7) The reference to Meritaten as "Mistress of your (Akhenaten) house."
First one should ask is there ANY OTHER EXPLANATION POSSIBLE FOR
THIS WORDING? The answer surprisingly is... YES! An adult daughter,
and Meritaten was an adult daughter, whose father is grieving as
Akhenaten surely must have lossing his mother, wife, daughter, and
Kiya all within a short period of time, often takes over her father's house
and runs it for him.
Personally i tend to view the younger Meritaten and Ankhesenpaaten as the daughters of Akhenaten and Bekeataten, and/or of Smenkhkara and Meritaten. For all the above reasons.
I hope this is a help Ankhesenamun3
