Honestly? I'd prefer the "Reapers gonna Reap" explanation for the Reapers: They do what they do because it's always done. They shouldn't need to be explained. Explaining them just weakens them.
That said, the synthetics vs. organics plot could have worked if it had been implimented better. Still would have been weak tea, but with a better implimentation it wouldn't have been so... horrible.
I probably would have preferred the dark matter plot above all else, though, albiet with some tweaks. Personally, I would have aimed for a variation on it:
1. Solving the dark matter problem is not the Reapers goal
2. Mass Effect technology is designed on
purpose to result in the destabalization of stars after many thousands of years of use in the galaxy. The Reapers built this feature in as a safeguard - Only the Reapers are capable of resetting the dark matter build up, and should the day ever come where organics are having success at fighting them back, those organics would start to see their suns destabalize and die in the middle of their war. Any organics that defeat the Reapers would also be faced with the daunting prospect of sovling the dark matter problem - which would give the Reapers leverage, if, somehow, they were ever at risk of losing.
3 . Miranda's fatther is actually Henry Eldfell, of Eldfell-Ashland energy. Eldfell-Ashland had been aware of the dark matter build up for some time, but was keeping it quiet, out of fear of what it could do to their profits. The asari energy consortiums had been keeping it quiet for much longer. Henry Eldfell joined with TIM because TIM promised Eldfell-Ashland Energy control over the Reaper's secrets on how to eliminate the dark matter build up and produce mass effect technology that doesn't result in that build up. Eldfell-Ashland would establish legal control over these technologies, making them the dominate energy company in the galaxy, and effectively giving them control over the galactic economy - at the same time as TIM, presumably, would use the Reapers to establish military control.
4. The above aspect of the ME3 plot would be stretched out, with one Priority mission dealing with this plot for every Priority mission dealing with the regular Reaper War. Miranda would possibly be a member of the squad to accomodate that fact. The "dark matter build up" problem and TIM/Henery Eldfell's attempts at controlling the Reapers would be unraveled slowly over the course of the game, in parallel with the missions relating to the war, until the two plots intersected towards the end. Missions on Novera that included Giana Parasini would also be involved with the dark matter aspect.
5. The final decision would be for Shepard to A) destroy the Reapers, knowing that he would destroy their secrets on how to mitigate the dark matter build up along with them, or

sacrafice himself to control the Reapers and presumably solve the dark matter problem - albeit possibly with uncertainty over whether or not he can keep true control of the Reapers in the long run.
6. The exact ending for

would also depend on whether Shepard is paragon or renegade. Renegade Shepard would likely use the Reapers to ensure human dominace of the galaxy - in line with TIM's goals.
The ideas are still a bit rough on some points, but they're what I've been tossing around, anyway.