Here's a total Salidar Rebels-Young Sitters-Tower Sitters-Anaiya-Kairen-Egwene Betrayed theory. There's a quick summary at the end, but you'll have to admit this is much shorter than other infamous theories I've had. Mostly cause I dropped all quotes. But you'll know what I'm talking about, right? ;)

Sheriam

I still don't see how anyone can not believe Sheriam is Black Ajah after reading her part in tDR. Her subsequent breakdowns and beatings only confirm what was hinted at very early in the series: Sheriam is Black Ajah.

Rereading the initial meeting between Siuan and the Rebels (FoH), something became apparent to me: Sheriam is in charge of the rebels. Sheriam is always the one who first gives approval to these new ideas. Sheriam is the first to say "we can't possibly go back to Elaida now," after Siuan presents her fabricated story.

I submit that Sheriam was forewarned of the coup against Siuan, and the Black Ajah commanded her to lead the Rebels and ensure division in the Tower. She is to take any steps necessary to keep the Rebels and Tower Aes Sedai separate for the next several months or even years. Wintering in Salidar was her plan, but Egwene ruined it by gaining control of both the Hall and Sheriam's council, and rediscovering Travelling.

Young Sitters

The Rebel Hall was chosen before Tarna (serving Elaida) or Aran'gar arrived in Salidar. The only people left who could influence the choice of Sitters is Sheriam and her council, Siuan and Leane, or the Ajahs themsleves. Siuan figured that Sheriam's council would have rein over the Hall anyways, so she may not have tried to focus effort on the Hall's selection. She was saving herself for influencing the future Amyrlin. As the organizers of the Rebels, Sheriam and her group could have had a lot of influence in pressuring Ajahs to select certain Sitters. Young Sitters are inexperienced, and may bow to pressure from Sheriam's council more easily. As head of the council, Sheriam may have tried to get Blacks put in the Hall, provided she knew of any in Salidar. But was her influence over the council, and thus the other Ajahs, that strong? Not unless they were all Black Ajah, which is supremely unlikely.

The Ajahs themselves may have second Ajah heads in Salidar, the highest ranking Sisters present, who chose Sitters personally. For the choice of both Tower Sitters and Rebel Sitters to be linked, advance planning on the part of the five bipartisan Ajah Heads would have been required when the Rebels fled the Tower, or the five bipartisan Ajahs have been communicating between the Tower and the Rebels since before a rebel Hall was Chosen. Perhaps someone can suggest a method, but I am pretty sure the timing for pigeons is too short, and other means unlikely.

Which leaves the Ajah Heads in the Tower acting together, independently of the Rebel Ajahs and their ‘Heads' working together or thinking along the same lines. The only known collaboration between the Ajahs among the Rebels has been in Sheriam's council. Which means that if there is a conspiracy amongst the Ajahs with the Rebels, either Sheriam's council directed it, they are minor participants in it, or they are unaware of it.

A clue is that Sheriam's council did not try to become Sitters. They know the penalty for forming a Rebel Tower, and want to retain power while not appearing to. The Ajahs must also know this, yet were faced with forming a Rebel Tower. Who to nominate? It is very possible that, independently, each Ajah realized that any Sitters would be stilled if all came to a bad end for the Rebels. So, dispensable Sitters were chosen. Sitters that are young and inexperienced, and who are rebellious in some way. Troublemakers, risk-takers and shit-disturbers. People who would propose linking with male channelers and stand for declaring war on Elaida.

If each Ajah did this independently, there would be no collusion between the Young Sitters. There doesn't seem to be any based on any votes they've taken. The Young Sitters vote on gut instinct, because they know their Ajahs aren't behind them. This was their one chance for power and making change. The Rebel Hall is a sham, designed to focus Elaida's attention away from those who got the whole rebellion going, just in case it doesn't work out.

Romanda saw the Rebels as a chance to seize power, and the exiled Sitters were still so angry they would not have given up their seats. They are committed to the rebellion, but if Romanda's faction balked (Lelaine's won't), then they have access to Elaida's emissaries at the negotiations, and can give Egwene up as a gift to spare their own skins. Ironically, now that Egwene is captured, they have nothing to offer Elaida in return for amnesty.

A clue that even the Young Sitters realize how tenuous their position is when Malind and Escaralde chose the back row, farthest from the Amyrlin during the Hall's last sitting. If usually it is desirable to be seated nearest where the Power resides, their sitting furthest from Egwene indicates a desire to distance themselves from the Amyrlin. Then again, that may have more to do with their proposal to meet with the Asha'man.

Tower Sitters

Note also that the Sitters chosen in the Tower also have the common characteristic of being not the obvious choice in some way. As though they were willing to risk the penalty for being Sitters in case Egwene's Rebels were to win. Also because they fear that Elaida or the Black Ajah has control of the Tower. The prominent sisters hold back while expendable, or unconventional Sitters are chosen. In this case, the Ajahs must have independently decided that Elaida was no longer desirable as Amyrlin, and come together soon after Elaida's orders stopped making sense to them. Except for the new Sitters, all other Sitters who were Sitters at the time of the split are now considered untrustworthy by their own Ajahs. The Ajahs are in essence, preparing a counter-coup against Elaida.

Anaiya and Kairen

Now the pressure is on the Shadow to keep the Tower divided and weak for the last Battle. Talk of negotiations with Elaida or the Black Tower is bad for the Shadow. They don't want the Tower reunited, and Asha'man can both make linked circles larger and can detect Aran'gar. Very bad news. Anaiya was killed with saidin the very night after the Rebels agreed to send an embassy to the Black Tower. It served three purposes: to create instant mistrust towards the Asha'man, to make sure the Blues would feel targeted, and thus not reunite the Tower, and a chance to reduce Egwene's power by getting rid of someone sworn to obey her.

Kairen was killed to prevent the blocking of Northharbor, as well as reinforcing the idea that Asha'man can't be trusted. With the harbor blocked, Egwene may have enough leverage to force negotiations ahead and reunite the Tower. With Kairen dead, Leane or Bode were the only ones left to do the job. Sheriam taunted Egwene with the idea that she couldn't send Bode, an old childhood friend, an attempt to stop the harbours from being blocked at all, and Leane was blocking Southharbour.

The only people with an interest in keeping the harbors open is the Shadow or Elaida. Elaida is not known to have any sympathizers among the rebels, though it is possible. Romanada's faction or a Young Sitter could decide to save their own skins. More likely, as a Sitter, Delana would have known the blocking of the harbors was to take place, and either she, Sheriam, Aran'gar or another Rebel Black could have communicated with the Blacks in the Tower to warn them, by pigeon or Travelling. Thus, Egwene was betrayed.

To summarize:

The Grey, Brown, Green, Yellow, and White Ajahs chose Young Sitters for the Rebel Hall themselves, independently of each other, in case the rebellion should fail. The Ajahs, and hence most of the Rebel Aes Sedai will quickly cease any support of Egwene as soon as it appears that Elaida will win, despite whatever their nominated Sitters in the Hall may decide. Egwene's betrayal was inevitable.

The Shadow's number one goal regarding Aes Sedai is keeping the Tower weak. No alliances allowed with the Black Tower, no reunifying the White Tower.

Both Anaiya and Kairen were killed to weaken the Rebel's position in negotiations with the White or Black Towers, as well as weaken Egwene's hold on the Rebels.