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.
An interesting theory...but I can see a few significant logical holes in it. For one thing, the only reason Jaavik's "wait till the dust clears" plan even got close to working is because it was supposed to be done in secret. The reapers found out (probably through the Prothean cycle equivalent of Cerberus) so they attacked and believed the facility wiped out.
So basically, there's no way the Reapers don't know that Cerberus has that area of space after the events of ME2. There's no way they can just hide there in secret. Even if they do ram the Omega-4 relay with Omega itself (very cool idea, BTW!) we already know they're perfectly capable of "walking it". It only took them two-and-a-bit years to FTL it from their darkspace relay to Batarian space, then another six months from the Bhak (sp?) system to the Batarian home system. Getting from the most core-ward relay to the galactic core may take a lot longer, but what's a decade or century to the Reapers? Plus, it's not like the reapers don't know where it is, right?
Another thing that might bugger things up is the Reaper vanguard. One assumes they leave one behind just for this reason and if Javvik's mission had gone according to plan, Sovereign would have jumped all over them. One can only assume that the Ilos scientists only knew about the use of a vanguard after the fact. So even if the reapers don't come to take out Cerberus at the core, you can be damn sure whoever they leave behind this time around will be sure to keep an eye out for them.
As it is, it's just a glaring omission. An omission that wasn't really helped by Gamble's Twitter canon - where he said that everyone of importance survived. Well if that's the case, would it really have killed you to insert a solitary slide as part of the end-of-game slideshow? Like the one above?
It's not error or oversight. Despite what they say, I can't believe they weren't aware of the glaring plot holes and dropped threads. They *can't* be that stupid. I'm convinced they knew they were shipping an incomplete product, they simply chose not to address them for budgetary/scheduling reasons. The release date push-back and some of the unused Londo dialogue files are pretty strong evidence of a mid-development triage and re-prioritisation IMO.