[Spoilers Extended] Maesters and the STAB alliance

When I read about how it was walys flowers who was the maester at winterfell, the one born of the arch maester and the hightower girl and that arch maester shown in AFFC was also involved with maester cressen (the one who wanted to murder melisandre) who was serving house baratheon as well since the old archmaester was always confusing the novice pate who was caring for him as cressen in his senile years(maybe because they were working together very often) that confirmed it to me that it was the maesters who were manipulating the information flow for the STAB faction during the rebellion.

Possibly the stark maester received the messages from lyanna about her going with rhaegar of her own free will but the winterfell maester probably either kept the messages hidden or worse gave a reply to lyanna and rhaegar as if it came from Rickard stark to make them relaxed enough not to do anything, the same could have been done by maester cressen of baratheons and potentially the Tully and arryn maester as well, who knowing the madness of aerys wanted to ignite the rebellion against the Targaryens to put an end to the reign of dragons in westeros and end the age of magic, and Rickard stark,Hoster Tully and Jon Arryn might have either knowingly or unknowingly went along with this plan of the Grey Rats.

it is a dark irony that the maesters and the citadel tried so hard to end the reign of house Targaryen and dragons only for it to blowback on their face and the dragons have returns and the rebel houses they supported are now close to the brink of extinction and without a centralized king to rally forces, Oldtown is most likely going to be conquered and sacked by the forces of Euron GreyJoy.