To defeat the reapers you need 2 ingredients. 1) a way to travel without being dependent on their technology, like your own jump gates or even better something that doesn't even need jump gates like worm holes or whatever and 2) a way to neutralize indoctrination. As it is you lose even if you win because just fighting them will lead to becoming indoctrinated eventually.
I like it how first two ME games established that Reapers are extremely powerful and even awakening them is almost a defeat, but then Bioware completely retconned it. Single Reaper fucks up united fleet in ending of ME1, but in ME3 you are engaged in trench warfare with Reapers and their biggest power is zombiefication now instead of brute force.
Again, in Revelation Space universe humanity had no chances in open combat with Inhibitors and managed to success by unleashing Gray Goo on them, but Gray Goo then went out of control and fucked up entire Milky Way galaxy. And only then remaining humans decided to leave the Milky Way and establish life elsewhere - in Andromeda galaxy, for example (isn't there a Mass Effect game in Andromeda galaxy?)