It seems that the main Mass effect writer was taken off the series after ME2 and put to work on Old Republic. If the reports are accurate, he did indeed intend for an ended revolving around the Dark Energy (even now that ME2 thread just left hanging is really bugging me). An ancient race turned themselves into the first Reapers (in the usual way) as a means of developing a solution to the Dark Energy that would consume everything, and they direct the technological evolution of other species and then harvest them in order to make new Reapers to add to their computational and implementational ability. This cycle was their last chance, and so the Collectors were made to scour the galaxy for a species that would make the perfect Reaper to complete this purpose, solve the problem and save all things. "We seek salvation, ours and yours." Shepard's choice would be to allow this, sacrificing humanity for the good of all, or destroying the Reapers and hoping modern civilisation can do it themselves. The ultimate Paragon and Renegade choice, though I'm not sure which is which.
Alternatively, this guy fixed the Reaper's origin, the star-child's identity, the purpose of the three choices, Shepard's appropriate response and the proper application of all those decisions and war assets in this spectacular re-write.