The part of Morrigan where she fears being a terrible mother like Flemeth rings true but even still, having her basically act the way she does at the Well justified in her mind that way, almost makes her as bad a mother as Flemeth?
Yep, although I don't totally agree with the theory and having thought on it some more, I'm still sticking with on my original take on things, elements of self-doubt are there true enough but for me the question is: would Morrigan let self-doubt crush her or instead use it as a life lesson and resolve to do better? You can easily infer that Morrigan herself recognises that doubt within herself and uses it as fuel to always strive towards being a better mother to her child than Flemeth was to her. That explanation covers the self-doubt aspect, marries it with her strength of character/survivor theme and let's her use it as a strength. That seems more like Morrigan, in a sense that she doesn't let her perceived weaknesses define her actions and that she's come to care deeply about those people in her life that brought about the change in her.
If say, the Well had some instantly terrible Indiana Jones and the Last Crusade style "He chose...poorly"
Ah, I have missed these random youtube videos that you used to work into your posts, good times 
Morrigan's actions in that case seem supremely self centered and kind of insane since up to that point its seemed like her main goal has been to keep Kieran safe. Like when you get to the Fade, Flemeth brings up how she's been searching for Kieran and yet Morrigan has up to that point kept him safe away from Flemeth. If that's been a big goal for Morrigan, I can't see how her going all reckless at the Well of Sorrows and potentially orphaning Kieran does any good. But like you said, if you color everything Morrigan is doing here through the lens of her own craptastic upbringing with Flemeth, maybe she's looking at this a bit selfishly, thinking she is just one step away from being a horrible mom like she felt Flemeth was to her growing up.
Yeah, that's a good counter argument and this is another reason why the Well sticks out like it does. As Flemeth points out, Morrigan has seemingly done a sterling job of hiding both herself and Kieran over the years, so to just randomly out of the blue decide that grabbing this particular power is more important than that, it doesn't really make sense. If she's been in Orlais for years, presumably using the resources available to her there to research and preserve old magic, why hasn't she enacted similar mad schemes in the past? Is she doing this now to help win the day, so to speak, could you say that since HoF could theoretically be threatened by Corypheus, helping take him out benefits her as well? I'd like to believe that could be a factor but we have the whole issue where BioWare won't let romance influence key story moments so that seems doubtful... Like I said above, on further consideration I think self-doubt/hate colours her actions to a point, but she'd turn it into strength rather than let it consume her, thus her comment at the Well regarding Kieran being better off without her maybe shouldn't be read into beyond that.
Coming back to my big post where I talk about how the whole thing is almost set up for Morrigan to take a fall - the title of that quest- "What Pride have wrought", is that a reference to her? As a play on the proverb "Pride hath a fall," in that moment she's so overly wrapped up in her own pride as the "elven lore expert" coupled with the lofty notion of preservation (without a goal, merely the means itself, rather than the end). In terms of romanced / motherly Morrigan it's forced and it comes back to how I talked on the devs really wanting to pull the rug out from under her but they seemingly had to make all Morrigan variants act in a pretty stupid and naive way to do it.
I just have issues with Morrigan's sudden reveal at the Well of Sorrows how she seemingly ditches everything to run head long into the Well of Sorrows for this really high minded and philosophical goal of blindly preserving all ancient magical things ever, just because. That really lofty, almost abstract notion of wanting to preserve knowledge and things just for the hell of it kind of bugs me since it seemingly flies in the face of how pragmatic she so frequently comes across in Origins. I guess it comes down to why she wants to preserve all that knowledge. Is it for some specific goal? Not really, since I think she basically says she just wants to save the world from the mundane. Which just seems... mundane?
Maybe this preservation thing harks back to Origins and her exploration of the wilds in animal form. Perhaps the key is that Morrigan sees the world through different eyes. Like how she mentions I think running through the Kocari Wilds in animal form, her desire to roam beyond the wilds, and her love of cities and other wonders, etc. If you go with that as a basic premise, you can kind of follow through on how she might not want unique "wonders" to slip away, yet in reaching for the Well, she loses Urthemial, so yeah... Maybe there's a sort of back to nature element to things, in the sense that there's something of a wild streak to her, perhaps she sees a sort of different beauty in the world that others do not appreciate? I dunno, like you say the wanton need to preserve things just because does kind of work against the pragmatic aspects of her personality.
Given how Morrigan (by her accounts at least) had basically an abusive upbringing, it kind of makes you wonder whether its like how you read about how children who grow up in abusive households have a higher chance of becoming abusive parents themselves. And maybe in Morrigan's case, she has a certain amount of self awareness of this fact, to the point where it becomes (again) an issue of self doubt. Or perhaps as kind of hinted at in the Fade scene, Morrigan did have some nasty or otherwise not great plan for Kieran originally but that changed as she actually raised him and started caring for him as her own child, not just some pawn or avenue for power or whatever her original plan may have been? And in reflecting on that, she carries a certain amount of ill will towards herself, maybe even reflecting back on how she's thought of how Flemeth seemingly raised her for Flemeth's own power by eventually stealing her body.
Yes, absolutely on the self-awareness comment, sort of already covered it in my earlier quotes. On the bolded point, one other interpretation is that she sees the Well as a sort of means to an end and since she's no longer willing to use Kieran to achieve it (the original plan), the Well's knowledge serves the same purpose maybe? But it does seem that Morrigan has sort of settled into a research & preserve type of mentality since after WH, mellowed I suppose, so much so that her original plan whatever it may be was abandoned due to his influence on her? A pertinent line from the game supporting the fact that she has changed her mind/plan would be - "In every way. At first, Kieran was a means to an end, but as he grew..." The simple fact that she was once considering using him as a means to end would play on her mind and also presumably make her reconsider doing the same/similar thing in the future. It really just ties and flows into the idea that by the time she faces off with her mother, she's a different person and wants no part in her mother's designs.
RIght- its maybe kind of how in your big post you mention the aspect of Morrigan having the high stakes and low stakes moments at the Well and later in the Fade with Flemeth. If we're looking at her willingness to drink from the Well as her almost giving in to her self doubt as a mother, as far as raising Kieran goes, then her slamming Flemeth in the Fade for being a terrible mother is sort of Morrigan's moment to pull a 180 and maybe realize that she isn't her mother and she can and will do a better job as a parent, even if she's not perfect doing it all the time.
Indeed, as a theory it does tie into (or at least compliment) my original post fairly well, I'd say particularly so when we bring in the bolded section, which I talked about above.
Yup, that's kind of my take on things. I guess taking a step back and looking at the overall feel of the whole Mythal sequence as a whole here given this new POV on Morrigan's actions, it still feels like a reach. I mean, I'm on board with Morrigan's whole crippling self doubt and her fearing she'll wind up a terrible mother like Flemeth. But I still have trouble really reconciling her actions at the Well of Sorrows, at least as they're presented in the game. If a mother/romanced Morrigan's actions at the Well are in part largely fueled by her being so self hating and fearful of herself that she'd take a blind risk, that should have come across much more than what you actually get in the game, which is basically that Morrigan wants to preserve stuff for the hell of it.
Agreed, I'm choosing to keep the self-doubting elements as a subtle subtext - it is there - "I never thought of myself as a mother, Inquisitor. I had no good example to follow.", but one that she has largely worked through by DAI (which ties in with the lines Ash Wind mentioned above) - "More than you can know. Kieran changed me. I will protect him to my last breath, if I must." and "In every way. At first, Kieran was a means to an end, but as he grew...") These are all direct quotes, it seems to me that all motherly Morrigans have the same resolve regarding Kieran.
It'd nag at her from time to time, but I don't think she'd let it keep her down or from doing right by her child. Thus the problem of the Well remains... Seems to me that BioWare needs to let some of those pesky old player choices and romance elements actually effect the big story moments, lest all these stated motivations begin to contradict each other.
I like this idea for her motivations as it does make sense, but I'm just wondering if we're not giving Gaider and company maybe a bit too much credit here.
Sure, I've actually had this exact point as a closing statement for many of the posts I've made but I've thought better of it each time. However, if we are reaching "indoctrination theory" levels of reaching in terms of trying to reconcile this, then maybe the answer really is what we originally thought - it's an out of character moment used to force a plot point. In which case one can't hold it against the character.
I have my high/low stakes interpretation on things which for me, fits fairly well, Ash has his idea on how she may have hidden knowledge on the well beforehand, which is somewhat believable too. Both though run into the problem of plot-dumb Morrigan, insofar as our lovely Elven Lore expert fails to make several deductions based on the available evidence in the temple of Mythal. Now a Morrigan with no power or ties, sure, I can buy into it, she'd take the risk, but the other Morrigan, she has more at stake, too much to risk on a gamble, I'd say, which is why her handwaving doesn't work for us. That it is the only thing in the game we can't reconcile with the whole suggests it is a contrivance and instance of plot hammer>logic. Or an instance of plot-induced stupidity, if you like. Which is sad because, if they'd have just had her refuse to do it after consideration - 2/3 extra lines, you'd lose the choice as the Inquisitor but she'd have been much more reactive to her past actions/choices and you'd have tangible evidence of your choices rippling through multiple games and we've be having a very different conversation.
Cue Sad Morri pictures:
There's enough sadness in the thread already with just the text without adding pictures into the mix 
Man, reading your posts keeps giving me idea for short fanfic scenes, because now I really want to see that scene where Morrigan has to explain to the HoF play out.
I'm glad they inspire you so
I'm toying with the idea of penning something myself, these discussions have scratched that itch. Not sure I'll go for such a dark scenario though, likely a series of shorts to fill in the blanks of some key moments from Morrigan and HoF's POVs from WH through to post DAI, if I follow through with it that is.