So I've been working on a complete theory of what Flemeth really is, as it seems to me like Bioware is crafting Flemeth into being the One, True Enemy of the Dragon Age universe. So I shall begin.
This theory shall hold that Flemeth is actually the result of a use of The Dark Ritual to imprison the soul of the Old God Toth from the Third Blight into a tainted unborn child.
So basically this theory started out a few nights ago, and I finally decided to post it up and get some input from other writers on here. Basically our first clue as players that something is up with Flemeth begins with our introduction to her. Flemeth is the keeper of the Grey Warden documents, for reasons uncertain. Naturally, this is only Bioware's way of letting us know that this lady is important and will continue to be. What about this makes me think she's an OGB? Well, it doesn't. Instead, our first hint comes from all the crazy stories about Flemeth. The Tale of Flemeth, her infamous deal with some entity which gave her the power to revenge herself upon Conobar. Nobody in the game can give us a straight answer about whether this makes her an Abomination or not, not even Morrigan. After Morrigan asks us to kill her mother, though, is when we get our big "oh, hi there guys" moment - discovering Flemeth can transform into a freaking High Dragon. Now we know by virtue of game development that pretty much all enemies in the game still fall into the classes of the players (Warrior, Mage, Rogue) and if Flemeth was REALLY a Shapeshifter (like the Darkspawn Shapeshifter in Fort Drakon at the end of Origins) then she wouldn't be able to become a freaking high dragon. There are only two creatures like them in the game - actual high dragons, and the archdemon. We recall now that The Old Gods took the forms of dragons.
There was, however, one other major clue: Morrigan. Flemeth's daughter is a skeptical woman, and she relies almost entirely on empiricism for her knowledge of the world. What I mean when I say this is that Morrigan wasn't bluffing or lying to the Warden when she offered The Dark Ritual to him. My Morrigan was in love with me, and she wanted legitimately to protect me, however other darker Morrigans still make the offer with the same certainty in its chances of success. Morrigan wouldn't be the kind of person to offer something she didn't know was going to work. How could she be so certain it worked? Perhaps she at first took Flemeth's word for it, but during her pregnancy (perhaps while studying Flemeth's True Grimoire) it became known to Morrigan that Flemeth was an OGB like the one she was carrying. This would explain her cryptic remarks about Flemeth in Witch Hunt.
DA2 only helped build upon my case. Flemeth being reborn from the amulet immediately should've made it clear that Flemeth was no Abomination. Anders, himself bonded to a spirit, was completely caught off guard by her return. Meanwhile, the old hag is there talking about how silly mortals are bound by bodies but she isn't. She might as well be saying, "I can be reborn from amulets and transform into a high dragon because I'm a freaking old god, you stupid meatbags." Then she gives you another cryptic warning which very well could be a hint that the world was about to be thrown into the Mage-Templar War.
Flemeth is the Old God Toth, from the Third Blight. Why the Third Blight and not another one? Flemeth doesn't appear until the Towers Age. What else happened during the Towers Age? The Third Blight. Assuming the presence of an Old God doesn't change the aging process of a human body (which may explain why Morrigan fled through the Eluvian to protect the OGB from Flemeth - or maybe the land beyond has a different flow of time alah DBZ Hyperbolic Time Chamber), then Flemeth would've grown up during Towers, being born in Towers 3:25-6. So who created the ritual and when? I've got a theory on that.
III. Research: A Grey Warden named Neriah
Neriah, according the game's lore, was a mage and Warden who was also the lover of Corin, the man who slew Zazikel to end the Second Blight. Why is she significant? According to the lore she died to save Corin from a magical bolt fired off from an emissary. I'm going to argue that she didn't die. Instead, she either faked her death, like Anders, or she used Blood Magic to cover her trail in history. She would then go on to create The Dark Ritual in her grief, claiming she would never allow another Grey Warden to be sacrificed for the sake of ending a Blight ever again. I think she probably used Blood Magic, as I believe it would take a Blood Mage to create the Dark Ritual. Obviously because she was a Warden she had a shorter span to get done what she needed to.
But, wait? Didn't I just get done saying that the Dark Ritual was used in 3:25 Towers? I did, and the game supplies me with the support - The Black Grimoire and the Invasion of the Body Snatchers spell. I believe that Neriah created this spell by studying the Archdemon in-depth, as she would obviously be doing so in order to create The Dark Ritual. She probably reverse-engineered the magic used by the Archdemon to transfer the soul of the user into a new body for a hostile takeover. This spell would give her all the time she would need to complete the ritual she was creating. She would use the spell to keep herself going until she could complete the ritual, hoping it would be before the inevitable Third Blight.
She succeeded in her plan. After going through the long, latent period of the Glory Age, Toth rose in 3:10 Towers to begin the new Blight. Neriah was even on the verge of completing the ritual, having had 115 years to study the Archdemon in ways no other could. The fallen Warden had all the factors that would be required to create the ritual. She had the means, being a mage was just the starting point - with access to the knowledge already compiled in the Grey Warden's archives from the process to create The Joining she could tap the most intimate knowledge gathered on the Archdemon. She had the motive, being the lover of Corin would've caused her tremendous grief at witnessing his death. The research she would be doing required Blood Magic, and the mind control powers of this magic school would allow her to cover her trail by manipulating those who write the histories and knew her - the perfect opportunity to research without anyone snooping.
On the eve of the Battle of Hunter Fell, Neriah approached a certain Grey Warden and made the offer to perform the Dark Ritual. This Grey Warden would've been someone that she'd been watching and perhaps manipulating with Blood Magic. She believed she was being a hero, and carrying on the memory of her beloved Corin. With the child conceived, all that needed to happen was for the Archdemon to fall. It didn't matter which Warden killed Toth, all that mattered was that the dragon die. Even she could do it, and perhaps she did - it doesn't matter. Neriah may very well have manipulated the scene to make it appear that another Warden had slain the creature (she wouldn't willingly kill a fellow Warden to set the stage, but she's not above necromancy [I think...]). Flemeth is born nine months later.
IV. Bridging "The Gap"
So what happens between Flemeth's birth in 3:25-6 Towers and when she marries Conobar, Teyrn of Highever? Well, I have a few possible ways that could work. Flemeth is born with magic as a natural gift from having Toth within her. Now, Neriah could possibly be shocked to see that the little girl was born with no trace of the Old God aside from her magical gift - this would follow with Morrigan's claim that the OGB was born an innocent in Witch Hunt. The other way around, Neriah could probably have created a spell to seal Toth's will. After all, she would probably have been the most well-researched expert on the Archdemon in the entirety of Thedas at that point. A seal would've been cake walk.
Now, problem is, something happens that permanently separates Neriah from her daughter. There are many different, interesting, and even heart-breakingly touching scenarios for how this happens. I like to think that Flemeth would've been raised with love by Neriah. She would probably think Flemeth was the child she and Corin could never have. Flemeth would've been her ultimate pride in life. The fallen Warden would teach her daughter all sorts of secrets the Wardens keep, such as the location of the ancient treaties in the Wilds near Ostagar and all sorts of magic. Something goes horribly wrong, though. Perhaps Neriah dies in a tragic, unavoidable accident. Perhaps someone finally put together the pieces of a mysterious and elusive puzzle, and was looking to find Neriah and the abominable OGB. It doesn't particularly matter.
Flemeth then makes her way, aged maybe between 16 and 21, to Highever where she eventually meets and marries Conobar. The rest is history. Fill in all the mysterious gaps. Flemeth awakens Toth, or breaks the seal on the Old God after witnessing the death of her lover. Perhaps having to watch the one thing you love most in the world die before your eyes was the key to the seal. Regardless, Flemeth gets her power from Toth and after slaying Conobar the Old God merges completely with Flemeth. Everything suddenly makes sense...