OK guys and gals here it is.

What is this object sticking out of the Crucible before it dock? Notice that it's round like a pillar and doesn't look like the prongs we see right as it is connecting. It's possible that this ejects into the citadel just as it docks.
Check this out. If Shepard was on the Citadel, then where are all of the features of the decision room?

They're not there because it's not part of the Citadel. I'll produce an image later but the energy that comes from the crucible flows down a cylindrical structure similar to that of the first image.
And look at this!

The prongs seem so expand but that cylinder is still visible. Shepard is standing on the cylinder. If this is true, this will explain how:
1) Shepard is breathing after he picks destory, the crucible has its own life support
2) How there are items from the normandy on the platform
3) And how Shepard is breathing before picking an option (Point 1)