I read the back and forth discussion and the main points of the Alleras=Aegon argument yesterday, and I am certain a few points have alluded me, but going back and reading the first and last POV's in AFFC with the theory in mind just seems to transform every reference to Alleras.
If it indeed plays out and the theory holds water then it makes for a brilliant and subtle piece of writing. In the prologue the boys banter about dragons while Alleras's only comments are obviously intended to change the course of discussion. He is pointedly ignoring the conversation, only to then state "I will tell you what I know of dragons... The dragon has three heads."
A page earlier:
"The Sphinx was always smiling. As if he knew some secret jape."
The prologue is full of such clues. Leo Tyrell refers to him as a lord's child, obviously suspecting he is of high birth, to which Alleras firmly states, "And I am no lord's son. I have told you. My mother was a trader."
When you read the prologue and then move on to the final POV from Samwell, more hints are furnished.
When Sam initially begins to tell Alleras his story, Alleras's seizes upon the name Aemon. "Did you say Maester Aemon?"
"Aye."
"Aemon Targaryen?"
In fact Alleras seems very interested in the Targaryens, telling the fate of the remaining family during the sack of KL in the prologue, telling Sam specific information concerning Aemon, and aluding to a specific interest in Dragons and things associated with them. More from the prologue:
"'Dragonglass.' Pate said. 'The smallfolk call it Dragonglass.' That seemed somehow important.
'They do,' mused Alleras, the Sphinx, 'and if there are dragons in the world again..'"
In the final POV Alleras demonstrates a vested interest in what to do concerning Dany, when Marywn finishes telling Sam the Citadel's anti-magic/Dragons perogative,
"'...Ask yourself why Aemon Targaryen was allowed to waste his life upon the Wall, when by rights he should have been raised to archmaester. His blood was why. He could not be trusted. No more than I can.'
'What will you do?' asked Alleras, the Sphinx."
I must confess I have not done a full research of Sarella or her history, but I will tentatively put forward the theory that all three are one and the same. It would seem to be most prudent to disguise the young Aegon as a girl while growing up among his "sisters" in Dorne, only to switch him to his rightful gender and reverse his name upon providing him a change of environment at a critical age when his disguise as a woman would be harder and harder to maintain. This portion of my theory is most likely easily debunked, but as I said I have not re-read everything concerning Sarella and her identity and supposed whereabouts.
If anyone can blow this out of the water then please come forward and sink my wonderful theory ship.