The reapers were pretty consistently established to be completely unbeatable conventionally, with a fleet that had more super-dreadnoughts than anyone had frigates. The writers put themselves in a corner from the very beginning.
They could have actually squeezed themselves out quite nicely (disregarding the invention of fucking
thanix cannons). The reason Sovereign was so devastating in the battle of the Citadel was not only down to its size and power, but because the Alliance had to close in so as to avoid inflicting collateral damage on the Citadel. This puts them in reach of Sovereign's very powerful beam weapons.
Take the Citadel out of the equation and put them in open space, then it's a fairer fight. The Reapers can close the distance, but they've got to run the gauntlet first (and that's without Alliance/Citadel ships backing up and buying more time). I don't overly care how powerful you are, getting slammed by a few hundred mass accelerator cannon rounds is going to ruin your day. And every Reaper ship destroyed is not going to be replaced for millennia.
As for the size of the Reaper fleet, whilst the end cutscene of Mass Effect 2 shows thousands of the bastards, you could actually leave it at that. Say there's three or five thousand of them. A terrifying force to be sure that would be invincible
if they controlled the Mass Relays, but in direct assaults they will get whittled down.
Ultimately, might sound strange, but a Reaper should be a bit like the KMS Bismarck in my view. Terrifyingly durable and heavily armed, but maintain distance, concentrate fire, and you can pelt it into scrap. Also, say whilst the Collectors have Oculuses, the Reapers might not in this hypothetical ME3 (the Collectors have probably had to fight engagements not nearly as stacked in their favour, so development of battle doctrine was necessary). In which case, the Reapers get a taste of carrier warfare.