Some different theories:
1) Both Ankhkheperures are Nefertiti under a new name, ruling as pharaoh. Some evidence of this:
- Ankhkheperure Nefernefruaten is sometimes spelled Ankhetkheperure Nefernefruaten--that is, in the feminine form.
- Nefernefruaten was one of Nefertiti's names.
- Ankhkheperure Nefernefruaten is called "The Beloved of Waenre." (Waenre being Akhenaten...)
2) Both Ankhkheperures are a young man (Smenkhkare). Evidence:
- No feminine varients are evident in the Smenkhkare (Ankhkheperure Djeserkheperu Smenkhkare) name.
- He was married to Akhenaten's eldest daughter, Meritaten.
- The body of a royal male was found in KV55. He was found to have died about about age 25. If this age-at-death is true, in could only be Smenkhkare.
3) Ankh(et)kheperure Nefernefruaten was Nefertiti as co-regent; Ankhkheperure Djeserkheperu Smenkhkare was a male ruling briefly on his own after Akhenaten's death.
This theory seems to make the most sense. I could see Nefertiti ruling a co-regent with Akhenaten, but I have a difficult time seeing her as a Pharaoh in her own right. I think the theory of the Ankhkheperures being two different people makes the most sense.
If the body in KV55 is Smenkhkare, then we know that he was a young man when he died, and that he is closely related to Tutankhamen, quite possibly brothers. Therefore, the question of Tutankhamen's parentage carries over to Smenkhkare. Most likely, they were both sons of Akhenaten by Queen Kiya. However, Tutankhamen and Smenkhkare could also be half brothers. Some argue that Smenkhkare was too old to be Akhenaten's son. Kiya was married to Amenhotep III before she married his son, Amenhotep IV (Akhenaten). Who's to say that Smenkhkare wasn't the son of Amenhotep III and Kiya, and Tutankhamen the son of Akhenaten and Kiya? I always thought that scenario was rather interesting; but it seems more likely that the two were both sons of Akhenaten and Kiya.
Late in Akhenaten's reign, Smenkhkare married Meritaten, th King's eldest daughter, who may or may not have been serving as her father or mother's (Ankh[et]kheperure Nefernefruaten) Great Royal Wife. Smenkhkare and Meritaten may have shared a brief reign (and Meritaten ta-Sherit could have been a child of this union) before they both died. If Meritaten died before Smenkhkare, he could have taken Ankhesenpaaten as queen briefly. Whatever the ambiguity, Ankhesenpaaten definately became queen when Tutankhaten became the pharaoh.