I mentioned a before that my theory is each Reaper, though its brain is made from millions of melted people, only has one consciousness, one mind. The Reapers only make one new Reaper per cycle, why? Because each Reaper's mind is taken from the best that cycle has to offer. At one point in the leaked script a Reaper said "We are all Shepards".
Why do you think they were interested in Saren, but as soon as Shepard proved he was better, they went after Shepard? They want the best. Why did they fail to make a Prothean Reaper? They couldn't capture Javik; the Shepard of his cycle.
Remember Shepard's line to TIM when debating saving the Collector base? "Next thing I know, you'll want to grow your own Reaper". That's exactly what he's doing! That's his grand plan in ME3! And what does a Reaper need? Three things: A whole lot of eezo for its core, millions of people melted into goo to form the brain, and a singular consciousness to form the mind. Cerberus has both.
Cerberus's only true goal on Omega seems to be mining vast amounts of eezo very quickly, with emphasis on the quickly. The rest of what they were dong they could've done somewhere else far more easily. Eezo core? Check.
Remember in Sanctuary, anyone not useful in experiments or as troops was liquified, and now we know why! Organic material? Check.
"Humanity needs your mind, and they need it intact". We never did have an explaination as to what that TIM did to himself, much less to this line. Now we do. Singular consciousness? Check.
This also gives a better reason for dream-TIM from a writing standpoint. We've already discussed how having a goodbye with dream-Anderson opens up the possibility of him being indoctrinated or killed, but this does the same for TIM, as next time we see him, he won't be TIM anymore...
These are also listed in order of least to most important, story telling-wise; it has proper build up. While you can do Omega after Sanctuary, that's a terrible idea from a plot and story telling perspective.
Also of note, the offical guide book for Mass Effect 3 calles the Control ending "Become a Reaper".