I also believe that Tutankhamen was the son of Akhenaten and Kiya. Who else could it have been? If you do the math, there is no was that it could have been Amenhotep III: If Akhenaten ruled for 17 years after his father's death and then Smenkhkare ruled for 2 years after that, it makes 19 years. Tutankhamen was 9 or 10 when he started ruling. How could Amenhotep have fathered a child after he was dead for 7 years?????
The whole issue there is the co-regency question. Some scholars believe Amenhotep III and Akhenaten ruled side by side for some years. The estimated time varies from scholar to scholar and ranges from some 4 years all the way to 12.
So IF there was a long co-regency, then it is just possible that Amenhotep III was Tut's father.The inscriptions left on behalf of Tutankhamen were just vague enough that he could have referred to Amenhotep III as his father OR as his grand-father.
Having said that I think that Tut was Akhenaten's son. It seems that he grew up in the North Palace of Amarna. This seems to be the palace of Queen Kiya (until she disappeared from the record).
And for as far as I know Tutankhamen and Cleopatra have nothing to do with each other. They lived separated by some 1300 years. Tutankamen was by all accounts of Egyptian descent, while Cleopatra was of Macedonian descent.