So I went back to play my ending and chosen destruction, got the little breathing scene at the end and all that, but I took some extra time to pay attention to what was going on in the final phases. If I repeat the theories already present, please bear with me.
After Harbinger nearly kills Shepard, they black out. When they reawaken, Shepard's armor is severely damaged, he/she is wounded, and the others making the run for the Conduit are dead. I looked around the area and the sqaud members are nowhere to be found at all, just dead Alliance marines. The pistol you have has infinite ammo, don't even have to reload it.
When you make the jump to the Citadel through the Conduit, you end up in a strange hallway full of bodies and it looks nothing like any place we've seen on the Citadel. I checked the piles of corpses and their all human, either with bald heads or wearing marine armor with the helmets on. There is no sign of Asari, Turian, Salarian, Batarian, Volus, Elcor, or Hanar anywhere.
When you arrive at the console, Anderson is already there, but the Illusive Man is nowhere to be scene until he walks up behind you. There's only one way into that room and even if the walls were changing like Anderson had stated, you should have been able to see Anderson before making it to the console. As soon as TIM shows up, you get the weird black vein edges on the screen and the Reaper-like growling sound playing, however this does not persist, only when TIM is trying to force his ideas on Shepard.
As others have theorized, it is likely that Anderson and TIM represent the Paragon and Renegade sides of Shepard's coin. Anderson is unable to act, yet he is saying lines that we would think the Commander himself/herself would say at the Illusive Man. TIM has the appearance of a Husk, even though through out the entire game up until this point, he shows no signs of actually changing in the slilghtest, and then suddenly he's got synthetic skin patches all over. At points in the conversation, whenever Shepard seems like they're resisting, you see the black veins and hear the Reaper sound, likely Harbinger's attempts to quash Shepard's will and completely indoctrinate them.
Both Anderson and the Illusive Man die, a figurative representation of not only killing the Renegade side of Shepard, also seeing the Paragon side collapse and die, leaving Shepard in an almost neutral light.
When taken to the top of the Citadel, there is nothing in that section that would suggest it has an enclosed atmosphere. Shepard is standing in the vacuum of space and BREATHING and not wearing a pressurized suit. In reality, Shepard should have imploded as soon as the elevator dropped him/her off.
The Catalyst's form is Harbinger's attempt to appeal to the more emotional side of Shepard's conciousness, to use the regret the Commander is feeling for having to flee Earth when the Reapers first attacked to trap the Commander into thinking that chosing either Synthesis or Control are the right options. Right off the bat, Catalyst intentionally says that they know he/she is there to destroy them, but goes on to say that it would not only destroy the Geth and any other synethtics, like EDI and those with implants, but also that it was not a solution to peace. "Your children's children will build synthetics..." is roughly the line Catalyst says, attempting to paint the Destruction option in a bad light as much as possible.
Synthesis is presented as the 'perfect' solution to the synthetic/organic conflict, but given how a Reaper is made, this is likely Harbinger's attempt to destroy Shepard's will by appealing to their sense of honor and integrity. painting a pretty picture that the two can co-exist by implanting sythetics and organics with a Reaperized version of Shepard's DNA. Control is the more blatant attempt at getting Shepard out of the picture and become a part of the Reapers, appealing to perhaps a more power-hungry aspect of Shepard's personality. We even seen the Illusive Man at the Control option, which is being made to appear Paragon while we see Anderson on the Destruction option, which is being made to appear Renegade. The two are polar opposites of the choices they are represented in, which raises suspicions about which is truly Paragon and which is truly Renegade.
Both Control and Synthesis leave the Reapers alive, something they want because they know that with the galaxy united against them, there's a chance they might actually be obliterated themselves. Shepard is the uniting force and if successfully indoctrinated, they can turn the alliances against each other to regain the upper hand. The Destruction choice is the only one that leads to the scene where Shepard is seen lying amongst rubble and taking a breath. I compared the damaged armor from this scene to the damaged armor for when you wake up after Harbinger leaves and the patterns are identical. The whole scene from after Harbinger's attack is an indoctrinated-induced hallucination that is testing Shepard's will to continue fighting or finally giving into Harbinger.
There's a lot of little details that really support the whole indoctrination theory and I'm hoping its correct. But please, continue discussing. Just putting in my collected thoughts.