The Catalyst is the Citadel respectively the Catalyst controls the Citadel, correct? Yet the Cataylst can't open the mass relay in the Citadel to let the Reapers re-enter the galaxy.
Making all of the events that lead up to the Reaper invasion seem completely pointless and grossly illogical is a feat that is really (isn't) hard to beat.
Just sayin'.
What makes you think the Catalyst had any direct control over the Citadel before the Crucible docked?
Being the collective knowledge of the Reapers and the overseer of the cycles residing somewhere within the Citadel doesn't necessarily mean it has complete autonomy over its functions. Those functions would make it easier to detect in its system, and it's clear that the Reapers designed the Citadel and the relays with a hands-off "guided evolution" approach in mind. How does Sovereign know that it's the proper time to signal the keepers?
Many criticisms you can lob at the relays not being shut off at any time can be lobbed at ME1, too. Why'd they build this thing without a simpler and more reliable on-off switch than a series of signals that can be hacked by the Protheans (which could have easily been done by previous more-advanced civilizations)?