The geth developed a self-repairing Colossus in a few hundred years.
Point taken, although said Colossus was destroyed off-camera before ME3 started by the Quarians, via a combination of their familiarity with Geth technology and authorial fiat.
You'll have to excuse me from thinking of the idea of permanently weakened, billion-year-old Reapers rolling into the knowing galaxy and getting conventionally defeated as being less believable than a super-weapon.
They don't have to be permanently weakened. A fleet of, say, a few hundred perfectly functional capital Reapers that got here by cannibalising fuel and/or discharge capacity from their comrades would still be a formidable threat to the Council species despite being a 'weaker' force than the crushing armada of thousands of ships that were presented in ME3.
Similarly a force of Reapers suffering engine damage would still presumably require time and resources to self repair. In fact that would add a nice sense of urgency to the game - stop the reapers before they regain their full power and become unbeatable again.
As to whether that is more or less believable than a super weapon... Well, that's a matter of personal taste. For me, the above would certainly win out. Particularly when the super weapon we're comparing it to has a couple of inexplicable additional functions including the ability to 'upgrade' every living thing in the galaxy with 'new DNA'.