As I've said elsewhere. I think the key to beating the reapers is to counteract indoctrination. After all we know the reaper ships have room for organics (cf Saren and Benezia on Sovereign.)
If they are are machines why wouldn't they be full of organic slaves to maintain them. Use elements already in ME1 like the Thorian research to come up with a a way to disrupt indoctrination and boom you can fight and beat a reaper
Ahh I say the secret should revolve around the mass relays like shooting a big projectile through one so it hits a reaper at a higher velocity than their sheilds can handle. faster than the way the guns already use the mass effect. or a ship could shoot out of a relay at high velocity and ram a reaper or something (which would be ther same thing.) by the way do the reapers use the relays? because if they do you could just blow the relays up that lead to them to stop them or something like that.
I think it will end with Duncan from DA:O popping up as the final battle begins and ceasing hostilities. The Reapers are just misunderstood, they only wanted to borrow a few cups of sugar to make a cake. It ends with Shepard, Duncan and the Reapers all breakdancing at a disco and eating cake.