That the 13 towers that the connection to the Shadow in the dream (why Egwene saw Mesaana's role in it) represents the Shadow behind the Paendrags. The Towers in Seanchan are a symbol of the Imperial's line power, foremostly. They were the first fortress of the then "invaders". In the dream, the symbolism has multiple concurrent associations The fall and rise of the towers do stand for the recent ups and downs of the Empire. Tuon almost died, her mother did and the central empire is in chaos. Tuon failed with Rand, but became a new hope to her people as Empress. The Seanchan stole Travelling, a major victory. The Empress herself can channel, and the people who know this are now in Tar Valon... it's a massive weapon for Egwene to use. She has what she needs to shatter Tuon's authority, even if Tuon has managed to seize Tar Valon at the time.

The middle Tower, in this perspective is Tuon, and is probably what Tuon will save of the Empire in the end. It could signify that in the Empire, Tuon will rise above any predecessor since Hawkwing.

The Dream also represents, IMO, the Forsaken, but only as the power of the Shadow they represent, behind the Seanchan, hidden. The Seanchan are an asset to all six who remain, and as we know, not Semirhage but Moridin himself has long been the mastermind manipulating the Paendrags and their beliefs and prejudices.

Egwene was only partially able to puzzle it out. She felt if Mesaana wasn't caught soon, something terrible would happen to the Tower. That interpretation confirms the Towers don't primarly represent the remaining Chosen. In the dream, Mesaana would be one of the Towers that fall as the central one rises, not a coming threat which needs to be averted.

I think a fuller but still partial interpretation would have been: Mesaana will find a way to exploit the Seanchan when they come to destroy the Tower, and we know the Seanchan are coming en force with that goal in mind soon. One of the Forsaken (Moridin) is an even greater threat to any alliance between Seanchan and Egwene. He knows which buttons to push to excite Seanchan who don't really need any more pulling, he put many of those buttons in place himself!

This dreams is just another chapter in the Egwene & the Seanchan dreams. It's a follow up to the dream Egwene has decided not to see to the end, because she couldn't accept that the outcome was that she needs the Seanchan and they need the Tower. She jumped out of the dream in the middle, never saw what was on top of the mountain, hidden above the clouds (the Light... rather obviously...) After her "failure", she got the consequence: the dream about the faltering lamp, the attack from the air. Now she gets an even more dire warning. She's not caught on the Seanchan connection, because the Towers of Midnight means nothing to her. She's just caught the bit about the Shadow being connected to that upcoming threat, Mesaana specifically. Egwene knows she's only partially understood what the dream was about - and she's noted that one down. There are Seanchan now near her, Seanchan who could mention the Towers by coincidence.

Accepting that this most hated enemy, that she has the best motives to hate viscerally, has to become an ally, for the survival of the Tower and the world, is probably Egwene's greatest remaining challenge in the series, both personally and politically. It's the part of Ishamael's schemes that concern the Tower most directly, and that is Egwene's role to unravel and correct. She needs to find a way to undo Bonwhin's legacy. It's the next step, after destroying Ishamael's Black Ajah. Another challenge Egwene may have in store (though for her this one might be the easiest) is the "Tetsuan challenge" : not to turn her back on that powerful Aes Sedai Queen, who's already attaching groups of channellers to her nation (in a way, challenging the Amyrlin's exclusive authority over Aes Sedai, which Egwene hopes to extend to all channellers), Elayne, who now cumulates the Rose and the Sun crowns. Tetsuan betrayed Ellisande the Rose of the Sun, out of jealousy of her power. Elayne has defied the Amyrlin's power before, binding the Tower in a bargain with the Sea Folk without approval of the Hall and Amyrlin. In a mostly symbolic gesture in KOD, she stripped the BA of their great serpent rings, noting in passing that she was usurping a prerogative of Egwene doing this... In appearance, though her reasons were real, she's refused to swear the Oaths and take the test for the shawl. Then, without warning, she twisted Egwene's plans, already in progress politically, for the Kin and, brushing off millenias of Tower neutrality, she's gone and attached the services of the Kin to Andor, negotiating her price with them for her protection... There may be an even greater clash coming soon between Egwene and Elayne than there was between Egwene and Gawyn. The Hall would have shread Elayne to pieces, but Elayne's fate will be exclusively decided by Egwene, an unforeseen consequence of her deal with the Hall, that placed dealings with the rulers under the Amyrlin's authority. Egwene will have to decide betwen stopping Elayne and maintaining the status quo of official WT neutrality, or if she decides to condone Elayne's bargain, she might be forced to offer the same services to all the other nations (which would be to the Tower's and the world's advantage, and is the most likely outcome). To spice things up, I more and more get the feeling that Elayne will change her mind and refuse to stand with the rest of the Tower in the debate over the breaking of the seals. If Egwene speaks for the whole Tower, as normally the Amyrlin ought to, Elayne might well commit herself to Rand's opinion nonetheless, as Queen of Andor and Cairhien instead of AS... Nynaeve might be the one in a bigger pickle, as she now committed herself to respecting Egwene's authority. Whatever they told Egwene, the WO will go where the interests of the Aiel seem to point, and Aviendha might shatter their beliefs about this soon... Egwene could easily see her "alliance" shatter in front of her, her efforts at re establishing the Tower's authory and extending it to the other chanellers threatened by the fact she opposes Rand's plans. I also get the feeling one of the "terms" Rand wishes to discuss with Egwene at the meeting will be the return to the their rightful place of the male Aes Sedai. He might ask that the full Asha'man are recognized de facto as full Aes Sedai by the Amyrlin. That would gain Rand a lot of Aes Sedai supporters all of a sudden Technicaly, the Hall could pull a fast one on Egwene too, they would be in their right to force her to put the final decision over the seals to a vote of the Hall. That vote may not go in the direction Egwene wishes, all the more if by some ta'veren twist the Hall is brought to accept it must give an equal or proportional voice to the male Aes Sedai... (in any case, I sure woudn't underestimate LTT's political cleverness... he's got ton of experience with civil governors and dealing with the Ajah and the Hall of Servants...