The whole problem is the ME trilogy doesn't have enough story for a trilogy. The Reapers aren't interesting or diverse enough for that. It's notoriously hard to write trilogies because one of them very easily turns out superfluous, so not having a clear arc from the start exacerbated the issue. Theoretically, it's a good model - each part of the trilogy corresponding to the classic 3 act structure. The issue in practice is that each of the acts aren't 33% of the story, and it's no wonder the hardest to write, act 2, more often than not turns out mangled. Shepard does the same thing 3 times, collecting allies in both 1, 2, and 3. That's why they needed to reboot the story 2 times, once with Cerberus and once back with the military. If I had to retain the skeleton of each of the parts, I'd do it like this -
ME1: Hunting down Saren and becoming a Spectre at the end of the game, which gives you enough influence to go searching for allies in the first place. You find out about the Reapers when you kill Saren, he warns you about them and tells you to find a beacon to prove it to the other council members.
M2: Collecting of said specialized allies with the authority of a Spectre backing you up in order to find the beacon, which should happen at the end of the game. However, seeing how you are becoming a bit of a power player and you not having a lick of evidence for these so-called Reapers, the Council hinders you at every corner.
M3: The beacon is located and there is no doubt about it - the Reapers are coming and they will be here very soon. Everyone knows this already and are preparing for war. Harbinger attacks one of the capitol planets earlier than expected and since basically nobody is ready for war, you are sent there to help out with the defense, but are unable to stop them and you flee the planet. This is when you go to Cerberus asking for their assistance and resources, they send you to sabotage the other capitol planets in order for them to be subservient to Cerberus during and after the war. Then the combined might of the entire galaxy manages to drive out the Reapers from the original attacked planet and blow up the mass relays the Reapers are going to use, so they can't come for another thousand years or so.
This leaves the ending extremely open to other entries in the series and the state of galactic politics in turmoil due to the now immense might of Cerberus. If I had to write the story from scratch, though, I wouldn't include the Reapers at all. Not every trilogy needs to be about saving the galaxy.