I just noticed that shinobi's ME3 wishlist in the OP focuses too much on the romance. I think we need a wishlist added for what we would wish of, and for, Miranda in ME3 regardless of any romance. I'll start with four elements that I've seen mentioned often:
Miranda non-romance wishlist:
(1) Miranda is defined, among other things, by her competence. She should keep that competence and professionalism.
(2) Miranda should keep her moral ambiguity. Her ruthless streak may be tempered or enhanced by some of Shepard's decisions, but it should neither vanish altogether nor dominate her character completely.
(3) Miranda must not suffer from "badass decay".
So, add your own elements to the list, or comment/correct the existing ones. The only restriction is that whatever you say should *not* be romance-related.
One element I'd like to discuss before adding anything to the list:
How much should her resignation influence her character?
There are two schools of thought about this: first, of course we want our decisions to have consequences, so she should change significantly. Second, Miranda is Miranda - regardless of what you decide, she always has doubts about keeping the base but also always has a ruthless streak. Also, the more Shepard shapes her through his decisions the less independent she becomes as a character.
If you follow the second school of thought, then, if she stays with Cerberus, she will do so reluctantly, which may result in her trying to change it from within. If she resigns, then she'll be glad to be rid of TIM, but she'll still think of her goal - doing something that profits humanity as a whole. She'll not be completely happy with either decision, which could result in interesting developments.
if you follow the first school of thought, then she'll probably be more content with whichever decision she makes. She'll be more Renegade than before if you kept the base, and be more Paragon if you destroyed it. In the first case, she'd become more like TIM, in the second, she'll lose a significant part of her ruthless streak.
Now, which would you prefer? I've heard many people say that they want her resigning to influence her character significantly. But I do not agree. Because I do not want her character to be so malleable, and because I think it makes for a more interesting personal storyline if the influence of Shepard's decisions on her character is more limited. And last but not least, because I like her as she is.