Could someone elaborate on the dark energy plot you speak of? I vaguely remember that being mentioned in the first game, but never being touched on again. The Reapers' motivations always seemed nebulous, though. First they're going to harvest all organic races because of dark energy, then because they use organic species to procreate, then because they need to keep organics from creating synthetics that will kill all the organics.
As I understand it, the plan was originally as follows:
1) There's a buildup of dark energy in the galaxy. The reapers are trying to solve the problem by allowing races to develop using their technology and then harvesting advanced races to build new reapers, and pressing the reset button on the rest of galactic civilisation to buy them more time for the next cycle by limiting the damage.
2) Shepard stopped the reapers from invading in ME1, delaying them. So they have the Collectors start building a human reaper in ME2 because the buildup is getting to dangerous levels and there'll be more stuff like the Haestrom sun as seen on Tali's recruitment mission.
3) Because humans are special or whatever, the latest human reaper would finally allow them to solve the dark energy problem once and for all, bringing the cycle to an end. Players would have been given a choice to destroy the reapers and try and have everyone find a solution to the problem in the remaining time, or let humanity be harvested to create a new reaper.
The reason why the actual plot is an incoherent mess is because, well, it's an incoherent mess. That's what happens when stuff gets changed mid-way by writers who don't know what the fuck they are doing.
With the original plot and a few changes you explain ME2's plot and why it was important, you have the foreshadowing in ME2 which makes sense, you get a way of defeating the reapers that doesn't come out of nowhere, and you actually have a reasonably coherent and interesting motivation, leading to an interesting choice for the player.