The Trollock wars did last a few centuries, probably the lifetime of a strong Aes Sedai and no doubt by the end of the war the Tower was streamlined and functioning but then peace came and stayed for a thousand years.

Government structures that are good at times of war can really suck in times of peace. Say the White Tower is turned into a weapon during the Trollock wars. Say the leaders are the best generals and stragists. Then peace comes.You might be required to help rebuild shattered communities Instead of having to fend off dreadlords you are being called to mediate on a boundary dispute or a trade agreement. Would a top general be any good at this? How do you keep your combat skils sharp if you have no one to fight in real life.

Yes they can go to the blight but apparantly the Shadow has home advantage on anyone who tries to take them on in the blight. Being an effective fighting force is more that just using killing weaves, its about groups of Aes Sedai being able to fight in a group effectivly and I don't mean linking but true team work. How do you keep the skill set that allows say 100 women to work in battle formation when all you have are isolated raids that come from the blight without notice and could be anywere. Your 100 formation can't be everywere. Even if you empty the Tower you can only have so many groups in real battle.

Without that skills grow rusty, beliefs and tactics are unchallenged and take root as sacred traditions. The new leaders are the sisters who can negotiate a trade deal or keep the peace beween nations. Then when war comes around 1000 years later you have to relearn all the lessons that the last conflict tought you but were forgotten.