Abit of what I posted before on my thoughts of Flemeth.
As for Flemeth's intentions, to me it's simple. The same goals she's had since she started down the path she's on so long ago. Power and Revenge. She seems to me to have the power part down pretty well. As for revenge, in my opinion, when you have the need of revenge, it's because of a great loss in some form or another. Revenge is a substitute for that hole left in someone from that loss, but it will never ever be filled. Like the Keeper in the Dalish quest ( his name escapes me, Zathrian I believe) his hurt was so great, that no matter what he did to fill the void through revenge, he never felt at peace (or does depending on your actions) and he is willing to go through great lengths to achieve his revenge, even sacrificing his own clan members in a round about way. Flemeth seems to me to be some one who is way past the point of peace, and revenge is all she knows. She states that she is at odds with what the world has done to her, and over her life time, it could've been a great number of things. So maybe Flemeth wants to finally make her move again. Rally her daughters and any who will join her cause. Not to free the mages from the chantry's power, not to conquer land and such (though it'd feed into her power to do so) but for pure revenge. To bring a hurt to the world like she's suffered. Thats just my thought.
The biggest game changer in my mind is Morrigan. She's obviously going to be a huge factor to Flemeth, more so than our Warden as shown by her story being almost guaranteed to continue compared to our Warden's who ends with Witch Hunt (I'm still unsure of how to feel about that) She is a complex creature like her mother, but not driven by revenge like Flemeth, though she strives for power. I believe her biggest goals as I see them are power and freedom. As a child, Morrigan always strove to explore and see the world for all it had to offer, but was always stopped short via fear, Flemeth, homesickness etc. Morrigan hasn't had the long life to experience all the negative aspects of life like Flemeth, and that brings to Morrigan a surprising amount of unhinted innocence for lack of a better way to put it. But like Flemeth, Morrigan values power, maybe because she needs it to achieve the freedom she's wanting? But Morrigan leaves so much unsaid and is extremely capable of manipulating others to achieve her goals. Who knows if she truly cared for our wardens, friendship or more that made that choice, maybe it was a front from the beginning to outmaneuver Flemeth? Maybe she truly did care, and that is the reason she warns you never to follow her after the Ritual, if players chose that path. The only absolute thing in my mind about Morrigan is the dark ritual. She wanted the Old God's soul, Flemeth's orders or no, and that was her sole purpose to be with the Warden. But again, because of player choice, the OGB plays a very, very tricky role in the DA universe. It could be nonexistent, or it could be a huge role player in Thedas history and everywhere in between. To me, Morrigan brings more questions than Flemeth.