Well, take a look at a lot of the stuff I've posted in the 'Foundation #8 Miranda' thread.
I'll start with a question: Why do you think Miranda would lie to Shepard about the clone in Citadel? Would you classify it as a direct contradiction to Miranda's word that was intentional? Or do you think it was simply an inconsistency in the comic caused by lazy writing?
I agree with you about that. I was just thrown off by the phrase "combined ME2-ME3 development". There's nothing in ME2 alone that would solidy swing in favor of telling him or not telling him.
And it is inconsistency, of the most laughable sort. But only in the phrasing. I don't think Miranda would lie, or better put conceal the clone at that point. I do think it was meant for testing only and was never supposed to be conscious, much less ambulatory so she'd be surprised by its continued existence and hostility. I don't think all that can fit under "just rumors".
They fucked up, pure and simple.
I simply prefer Miranda knowing about the clone to not knowing. For once, that's all.
The case can be made that she should've known. I suppose at the end of the day, the best interpretation is what we're saying: she was aware of it being used for testing but she expected it was destroyed when the real Shep came back.
I don't feel any need to reconcile the two, any more than I feel the need to reconcile Samara's statements on ardat-yakshi with the fact that there are way more than three. At best/worst, I might use it as an excuse for them to break up in a fanfic. But mostly, it's just another retcon.
Different situation altogether. There are in-universe reasons for Samara to be mistaken or evasive on the number of ardat-yakshi. There is zero possibility of Miranda being mistaken in this case and zero reason to conceal. Not to mention that if Miranda wanted to hide something she can do better than "just rumors".
I mean it's not like Shepard was brought back in the same way that Agent Coulson was.
Haven't kept up with Agents of Shield but just in case I go back, please no spoilers.