There is an article over at Kotaku about the series' villains and unfortunately their service had an error that prevented me from adding a little something to the Cerberus organization, so I'll post it here.
The problem with Cerberus in Mass Effect 3 was that the writers didn't take the organization's "humans first" ideology to the extreme, instead resorting to the vague, out of nowhere and totally out of place "Control the Reapers!" plot point that didn't amount to a hill of beans.
Than I thought about the Collector Base in the center of the galaxy. What if Cerberus, in their attempt to make mankind the dominant species in the galaxy, actually 'allowed' the Reapers to go through with this cycle of genocide? What if the Collector Base was just a ruse in order to deceive Shepard into ensuring TIM's bigger plans for that part of space? Whether the station was destroyed or not, Cerberus would have control of that region of space. Think about it. If Cerberus could inhabit that area of the galaxy, seal it off and hide there till the Reapers were done with their cycle, than humans would not only be the dominant race, but also the only technologically advanced race in the galaxy. And with their knowledge of the previous cycle, they would also be prepared for the Reaper's next cycle.
This sort of planning would not only explain why Cerberus is sabotaging everyone's efforts to stop the Reapers, it would also explain why Cerberus specifically took over the Omega station. They wanted control of the system that housed the Omega 4 Relay, which was the only means of safely entering that region of space. Once everything was set and the galaxy was beyond hope of fighting the Reapers, Cerberus could have destroyed the Omega 4 relay just as Shepard destroyed the Mass Relay in "The Arrival" (Wow. This idea even justifies that DLC's existence!) and remain totally isolated from the rest of the galaxy, even the Reapers.
And imagine the kind of realization that Shepard would have when she realizes that all the things she tried to accomplish in ME2 only resulted in Cerberus' benefit, not the rest of the galaxy's. She would have unknowingly set in motion events that would doom the other races of the galaxy including a majority of humans who believe in alliances and unity with the other races. And to make it worse, TIM would be congratulating her for it and even have her be remembered as a hero who made all of it happen. Cerberus' future humanity will never know of her alien allies or the alien worlds she worked so hard to protect, because thanks the Reapers their entire existence will be wiped out.
But instead of anything like that, all we end up with is a jerk who does nothing but gloat and ends up killing himself. Way to go on the "His weapon is his intelligence" route on that one Bio.