I'm a wee bit surprised that we haven't had any real speculation on the subject of the citadel and the conspiracy, so I guess I'll started us off. While I had my own ideas I actaully rather liked this one I got over on BSN.
In regards to this DLC bioware have said they have been listening to fan and from the sounds of things they are delivering (IGNORE THE ENDING!!!!) so apart from more interaction with past squadmates what else has been on the fan agenda, well Harbinger having a larger role, maybe he's the antagonist in this DLC. But think in regards to conspiracy (not the Cerberus coup) that has plagued ME3 since launch (at this point I'd imagine most of you have a good idea of where I am getting at and are all ready dreading it).
That's right the Indoctrination theory (IT) now I am not talking about the actual IT but think about it a conspiracy involving Shepard, what's more a conspiracy than Shepard being indoctrinated, which forces Shepard and his squad to clear his name with the aid of the ME2 members and Wrex as they hear about the ludicrous notion and rush to his aid. It's the last DLC, a last change to put the IT down for good, what better way then to tackle it head on in game. (Then again we all thought of Leviathan and the EC and look how well that worked.)
So that's my idea but what's your idea on the matter.
Edit 28/02/2013 So spending more time over on BSN it had come to my attention that the main villain is apparently someone we already know and has a good reason to hate Shepard. So Thoughts, if this is indeed true.