To me I wouldn't mind setting up Miranda's appearance in ME3 in a manner similar to Tali's in ME2. Reintroduce her character in the first act, only to have her fully appear either later in the first act or at the start of the second.
From what we've seen so far the start of the game is Shepard's trial on Earth. It would make sense that Miranda would leave the Normandy before it reached Earth because a) Being a potential former member of a terrorist group isn't exactly the best thing to introduce to a millitary trial and

Mr. Lawson is still on Earth, best to avoid his forces.
It could also set up the whole "dire consequences" aspect for people who "cheated" on the VS with Miranda. If we have the VS with us from the begining of the game, and given Shepard's seeming inabillity to talk to people about relationship problems unless he's being shot at
(see Horizon or LoTSB) There's a good chance that things will be looking on the up and up with Shepard's relationship with the VS until Ms. Lawson returns...
Ash: Who's she?
Shepard: Miranda Lawson, she was my XO when we were preparing to go through the Omega-4 relay.
Ash: She's with Cerberus? I thought you were done with working for them!
Miranda: Actually, I don't work for Cerberus anymore. I thought Shepard would have told you that.
Shepard: I should go.