User blog comment:Suparockr/List of Plotholes throughout the series/@comment-99.231.255.41-20130418174351/@comment-173.58.251.107-20141103193220

Saren can't activate the Citadel Mass Relay when he was still trusted because he didn't know what the thing was and where it was. Sure, Sovereign could have told him where the mass relay control panel is, but there is basically almost always someone in the Council Chambers, so if he tried to do it, someone could have come along to stop him.

Two, Saren and Sovereign had to issue of the Conduit, both thought it was something that could either help or hinder their plans, so they had to go looking around for it. Also, Saren's goal was to save the galaxy, he could have believed the Conduit would allow him to do this, and Sovereign had no idea what it was, as far as it was concerned, the Conduit was an anti-Reaper weapon, so it had to deal with that first.

Three, Sovereign was perfectly aware that if it attacked the Capital of the Galaxy singlehandedly head on, it was going to die, without anyone inside to lock up the relays or an army to distract it's enemies, the entire fleet would just turn it's firepower on him and that'd be the end of it. Vigil said it itself, Sovereign, and any Reaper by extension, is powerful, not invincible, a fleet can hold it's own against a single Reaper, and indeed it did.

Four, The Reapers are meant to preserve life by storing their data and cultures in Reaper form. By doing this, the race effectively lives forever, as they are now in immortal Reaper bodies as opposed to their mortal bodies. The way they go about preserving the life is what doesn't make sense. Why kill organics to save them?