I'm still wondering why no one thought of just dropping several EMP bombs in the middle of the Reaper fleet. If they're machines, that should fry them pretty good. Might not kill them since we know they're also organic, but it should as least slow them down.
However, since we know that is not going to happen because the odds are that the Reapers have some sort of defense against that, I see two possibilities.
1) As the hologram on Ilos pointed out, the Reaper's main advantage is surprise. They storm in, crush the head of galactic civilization, and the body slowly dies. When Shep asks why they do this, the hologram points out that, while powerful, the Reapers cannot stand against an united galaxy and they know it. That is why they crush the leaders in a surprise attack. Well, Shep stopped that from happening, and if the previews are any indication, the Reapers are going after Earth first. Which means the other races will be left alone. It's going to be Shep's job to unite the other races while the Reapers are focused on one target, and then use the entire galaxy to counter attack. After a massive death toll, the Reapers will be defeated. BioWare already wrote in their defeat in the first game in order to avoid the situation you're talking about.
2) As others have pointed out, BioWare cheats and introduces some sort of super anti-Reaper tech that helps greatly. I must admit I'll be a little annoyed if this happens because it's a cheap way out, and it also raises the question of why no one before the humans thought to use this weapon.