Sovereign's been at this for, what, fifty years? Longer? Here's how I always figured it:
The Reapers were supposed to arrive decades ago, but didn't because the Protheans shut down the Citadel Relay. Sovereign sent the signal for it to open, it didn't, and he flipped out. He's spent the last several decades trying to seize control of the Citadel so that he can get it open again, largely improvising with no communication to the fleet because the whole plan went to shit.
Meanwhile, out in the depths of space, the Reapers realized the Citadel Relay wasn't working, started trucking it to the galaxy the hard way, and have been doing so for the last several decades since the Relay failed to open. Had Sovereign succeeded in opening the Citadel Relay, he would have been very shocked when absolutely no Reapers appear, because nobody's on the other end; everyone's on their way through the long path.
Sovereign was left behind with instructions on, "Do X," and he did, and when it failed, he panicked and scrambled to figure out how to fix it, while the rest of the fleet was busy fixing it their own way. Inability to communicate and coordinate their activities resulted in the right hand having no idea what the left was doing. The entirety of Mass Effect 1 could have been avoided if Sovereign had been given contingency instructions of, "dick around for several decades, do nothing to give our existence away" in the event the Citadel Relay shuts down, but I get the impression that he wasn't because nothing like this has ever happened before. The system not working flawlessly is unprecedented.
The same can be said of the rachni war, the krogan rebellions, even the First Contact War...really, most things that were shit about galactic history in the last few decades can be traced back to Sovereign panicking, not having any idea how to fix things, and desperately improvising. The fact that the galaxy was even able to put up a fight against the Reapers in the first place can be attributed to the same. The Protheans broke the system, Sovereign royally screwed up - and devastated the galaxy - trying to fix the system.
edited 11th Dec '13 7:58:07 AM by TobiasDrake
In some fantasy cultures, the Rainbow tastes you.