I agree with Eain that the conduit is probably a plot hole in ME1. My personnal "in game" explanation is that reapers are methodical, and didn't want to launch an invasion without knowing what went wrong. And that was Sovereign downfall because it tipped Shepard off.
My personal "out of game" theory about what happened however is that the conduit originaly lead to a sealed off section of the citadel, only accessed by keepers. And that zone was a near release cut in the game content.
2 reasons :
The keepers have a tendency to clean up things on the citadel. Stands to reason that a prothean-built mass relay exit point on the presidium wouldn't survive a post reaper invasion clean up.
The mass relay fonction of the citadel had to be manually reactivated. It would be logical that those hidden controls would be in a zone never accessed by other species.
Of course, no proof one way or another, so I'll leave it at 'that's my opinion"
EDIT : In fact, I messed up withe Reason 2. Sorry.

Sovereign intended to activate the relay himself so it COULD be done remotely once plugged into the citadel. The remote zone could however have to do with the keeper modification / keeper control of the citadel. And I stand by reason 1:ph34r:
Modifié par Yzzid, 01 avril 2011 - 02:24 .