The Reapers were never that powerful. The whole conceit of the series is that they have developed a complicated trap to ensure their victory. A trap that is thousands of years late, and now the galaxy has a dead Reaper to study. The capabilities they display in Mass Effect 3, by flying in from dark space and reaching every homeworld in the space of a few hours, essentially renders that trap pointless. The lore in the codex even provides reasons that could set up the Reapers being vulnerable, such as the need to discharge drive cores because they're still just big starships (which is the first thing we see Sovereign do in the series) but Mass Effect 3 handwaves all of that, too. Mass Effect 2 is basically about Harbinger deciding that it's more efficient to try and build a new Reaper from scratch and go after the Citadel plan again rather than fly in from the edge of the galaxy.
I think what Bioware should have done was a Mass Effect where the Reapers have arrived but they're drastically reduced in numbers or power due to the flight from dark space, so they're desperate, but they can be defeated. But they're still strong enough that it could be mutual annihilation if Shepard/the player doesn't get enough war score. Elements like that are why Mass Effect 3 is more of a failure than just the ending, but are the errors that players can easily overlook. The ending being a ghost kid telling you to pick a color situation less so.