Well I had posted this a while back, but it was strangely locked, so I decided to put it back up.
Anyway, I was thinking about Varys' character and had an interesting thought which really put together some of the pieces of the puzzle wrapped in a mystery wrapped in an enigma that is Varys Blackfyre. Varys is a woman and Joffrey's mother. Here are my answers to some questions you may be asking:
How can Varys be a woman?: Varys took some hormones to appear slightly more masculine, which were supplied to her by Kings Landing's medical genius Qyburn, whom it is generally accepted is on Varys' payroll. Creating the right hormones, or something similar, shouldn't be difficult for Qyburn, who, in addition to being a medical genius, can also perform some sort of magic/sorcery, like with Gregor Clegane/Robert Strong. Then, Varys concocts an elaborate tale of being a eunuch who was castrated in some magical ritual so nobody notices a bulge, and she says that she lived in a far away place when it happened so nobody can unravel the elaborate tale she wove. Then Lady Varys seduces Jaime and has the children with him, who are blonde because both Jaime and Varys are blonde, or a least Varys was blonde when she had hair, as she is a Blackfyre.
If Varys took hormones, why does she still appear so feminine?: Even though she took hormones, it doesn't completely do the trick of making her seem like a man, so she still seems rather feminine, especially since whatever she took would be made from medieval technology, and wouldn't be at the standard of modern hormonal serums created by scientists. This also proves that she was never a man, as it is a medical fact that a male losing his male genitalia would not makes him appear any more feminine.
Why is Cersei so vindictive?: She believes the children are hers, but deep down she know's something's up, but she can't quite put her finger on it, so she is always teeming with rage. This is why she takes out her rage on her children, like the awful way she treats Tommen.
Cersei believes she was pregnant with the children, how is this possible if she's not the mother?: Well, it's not exactly hard to convince someone as mentally unstable as Cersei that she was pregnant with regular doses of milk of the poppy, or perhaps another mind altering serum, supplied by Qyburn, and gaslighting.
Why is Jaime is so guilty about his relationship with Cersei?: Someone who doesn't mind killing children wouldn't feel guilty about fucking their sister, he's really guilty about lying to Cersei the whole time and telling her his children are hers. And it also explains the inherent sexual tension when Jaime interrogated Varys over Tyrion's whereabouts. It also explains why Varys helped Tyrion in the first place, it was because Tyrion is the uncle of her children.
Varys being an apparent eunuch is an allusion to the fact that Illyrio (Varys' brother) is a eunuch: This explains why he eats so much, as food is one of the few vices available to eunuchs. Illyrio was castrated because during his tenure as Prince of Pentos, a tragedy befell Pentos, and as we all know, when a tragedy befalls Pentos, the current Prince is killed and replaced, but Illyrio's extreme wealth was enough to pay off the Magisters of Pentos, and got off with only being castrated, rather than losing his life.
Jaime's children by Varys, a Blackfyre, are direct descendants of Aegon I Targaryen: This means that they are the three heads of the dragon. The first head, Joffrey, had to die for the other two, Tommen and Myrcella to continue to live, as a reptile cannot live with more than two heads, even in real life, there are two headed snakes but not three headed snakes. Joffrey dying secured their continued living, as if Joffrey lived he probably would have had them killed in a fit of madness. This also means Joffrey, along with being a head of the dragon, is Nissa Nissa, he was sacrificed for the other the other two heads, his siblings.
Varys is the younger, more beautiful queen: This is because, in the eyes of Jaime, the only person who's opinion Cersei ever valued, Varys is more beautiful, hence why he chose her to be the mother of his children rather than Cersei, and Varys will be Cersei's downfall.
Why would Varys have Jaime's children?: Varys' motives for having Jaime's children is to sow discord in the usurpers ranks and pave the way for fAegon's ascension to the throne, who is Illyrio's son, and Vary's nephew.