I think at this point hallucination/indoctrination may seem a bit unlikely. Still, it's a nice thought, and there's certainly stuff that seems to back it up. On the other hand, it could simply be that they weren't sure how to end it properly, and simply messed up with holes in the available options and the supposed logic of the child (and even why the Catalyst was the child). It's nice to think though that the dream-sequences were specifically intended as a hint though.
Still, I think the connection with the Crucible makes some sense; since it seems to line up with the circular part at the base of the council tower, which is where the control panel and weird engine type thing is. It seems strange that no-one would have noticed it sooner though, give that a shuttle could easily have done a fly by and seen a weird platform, though I suppose it may not have been active as a control panel till the Reapers took over, but then, why would it be so close to the area where bodies are teleported in? If you want to put a control panel that secures the Citadel somewhere then there must be better choices (like the top of the tower where Saren accessed one, for example). It still doesn't explain why those human-tech pillars are in the base of the council tower though, unless it was part of a human effort to repair the Citadel after Sovereign's attack; that does seem a bit tenuous. It also reminded very heavily of the pylons on the Shadow Broker's ship, along with the sliding segments that were in the ship's engines. Might just have been re-using assets to save time, I dunno.
I don't think the teleport beam would have sent Shepard to the Crucible, as that doesn't seem to make much sense, and neither would the destroy/control interfaces for the Reaper tech. On that note though, there is a hole here too, since the Prothean VI mentions that a faction amongst them argued for controlling the Reapers, but it seems like they were catered to already if the Crucible did include that option in its construction; but then why would this splinter faction have interefered with the Crucible in that case?
I do think that the scene up until Shepard opens the arms was real, as the Illusive Man seems heavily indoctrinated and it seems implied that he's preventing Anderson and Shepard from acting until Shepard is able to distract him enough to fire. The pylons in the area on the Citadel are an oddity, but I think if the end is a dream sequence then it most likely plays out from when Shepard collapses in front of the console, and could even be some close to death delusion.
The whole ending is a bit of a confusing mess, so having it be some form of indoctrination wouldn't be so bad. Sure people would be disappointed at the game having been incomplete but a replacement is still very much called for IMO. Having it being a dream-sequence is a bit cheap, but it could easily fit. I dunno though, it's a nice thought but I'm not sure I'm completely sold; personally I suspect it happens as it happens, and would rather just see changes to the end options based more heavily on your actions in the game.