So I just finished ME2 in my usual way of Paragon base keeper who romanced Miranda. One of the things that I initially attracted me to her was that she wasn't in need of salvation. She was plagued by low self-esteem, but she knew who she was and what she wanted out of life. She had a cause she believed in.there's a part of her that needs to be attached to a cause to validate her existence, but in the last conversation you have with her–the conversation where she's at her lowest point regarding her genetics–she gives her reasons for joining Cerberus as essentially needing a challenge. It's not just latching on to the first group that will give her approval. And, if you dump her, she takes it rather well. This is a woman who cares about you, but she doesn't need you. Kasumi notes a change in her, but it's that she's a happier person. And indeed, she is a good bit happier if you Paragon her LM.
And somewhere around LOTSB we shift to a salvation story, with Miranda being redeemed by love both filial and romantic. Liara remarks about how much you've changed her in a romance from being "cold" and "completely focused on her duty." This suggests more than mere happiness. It suggests a change in priorities. Not merely a change in allegiance, which is justifiable and by ME3, morally necessary. This is Miranda shifting her focus from serving an ideal to being motivated by love and family. Her dossier supports this. Dropping a subscription to scientific journal is paired with subscribing to a fashion magazine and buying a relationship self-help book. Now there's nothing wrong with fashion magazines or self-help books, but the arrangement suggests that Miranda is finally getting in touch with what she really wants and what she really wants are traditionally feminine things. The dating and medical sections of the dossier suggest similar lines: Miranda discovering that what she really wants is a family, going about it with the social awkwardness nowhere present in the main game, and being cruelly denied it. It's also notable that the SB writeup on her paints her as a much nastier piece of work than the main game does: "ruthless" and "obsessed with human dominance." She is no longer merely mistaken in believing that Cerberus fights for her stated goal; her goals themselves are now suspect. Suddenly getting interested in fashion and children (and Shepard) is a good thing because it pulls her away from her evil goals.
And sure enough, ME3 Miranda is entirely motivated by her love for Oriana. Mentions of her Cerberus past are cursory at best, to the point that a Shepard who kept the base (ie, one that wasn't directly responsible for her celebration from Cerberus) will have no idea why she left. The idea of her only wanting marriage and children is picked up again in the death scene with the "things I can never have" line. Now, you may say that that's only indicative of the normal life she wanted for Oriana, but she still never mentions the things she wanted for humanity as a whole. Her goals are entirely personal. If she dies, Liara will speak of her coming to the right side in the end. The whole thing suggests that she was morally corrupt before but that her love for her sister saved her. If ME2 Miranda were to turn against Cerberus, I believe it would be ultimately because they turned against her ideals first. ME3 Miranda does not turn against anything. She merely hurts the people who are hurting her sister and just happens to stumble into a major contribution to the war effort. Several times, I feel like I'm supposed to give her moral credit for not being a sociopath. She loves her sister. Lots of people do. She shut down the ME version of Auschwitz, but she didn't go there to shut it down. Once she was there, she did, but I would expect no less of a supposedly capable operative. For all her abrasiveness and alarming quickness to declare allies expendable, Miranda showed more care for humanity when she was a Cerberus operative than when she was supposedly a better person.
Which leads me to my last point. We've talked several times about the fact that it felt like the writers were telling us that she needed to die for her crimes. But, well, what crimes? We know of exactly two operations she was involved in prior to ME2: saving the Citadel and resurrecting Shepard. She's more of a unsung hero that a villain. She's rude and quick to write her allies off as expendable, but she's no worse than the Renegade Shepard. In fact, she frequently voices the Renegade option in a briefing. Her choice may lead to a sub optimal outcome, but her choice is usually at least possible for Shepard to enact, unlike Jacob. On some level, the writers realize that she just wasn't that bad, because her confession is only the something she thought about doing. Now there are things a character can do that mean they "have" to die. But those characters really, actually, have to do something. Not merely think about it.
ME3 Miranda is not ME2 Miranda and the two games aren't telling the same story about her.