I think the question here is what exactly did we accomplish in ME2? Destroying the a new Reaper (if it is indeed just another Reaper) isn't especially significant if there are hundreds or thousands more of them. Likewise, destroying the mechanism for making new Reapers isn't actually a big deal because the Reapers can just rebuild it once they've secured the galaxy (that seems to be their preferred strategy--secure the galaxy quickly, then take their time harvesting).
One of the key points from the other thread is that the galaxy/universe is a really big place, even relative to having FTL capacity. The mass relays are key to getting around that limitation, and it was mentioned (back in ME1) that one of the reasons the Reapers take the citadel right away is to shut down the relay network, leaving their victims cut off from one another and unable to rally their fleets. The advantage is huge, and effectively wins the war for the Reapers immediately. That, in my opinion, is why it makes sense for the Human Reaper to have been another vanguard--another attempt to seize that crucial advantage. Sure, everyone had seen Sovereign, but pretty much no one but Shepard really believed it was anything more than a Geth ship; accordingly, the Collectors killed Shepard, ending the threat to their masters. The citadel fleets might have been more wary of attacks, but the Reapers still had a massive fleet of Geth at their command (once the reprogramming virus was used; stopping the virus is one major thing you *might* have done in ME2), and they only had to win one battle to win the war.
Once the Reapers know that Shepard has been brought back to life, and they can no longer make a new vanguard remotely, then it makes sense for them to abandon their plans of using the citadel relay. If the Reapers had already given up on that plan before losing the base, then what exactly was it that Harbinger said they would "find another way" to do? Is there something else that we haven't seen at all, or was that just getting the lore confused (i.e. whoever wrote that line thought that the Reapers hadn't started travelling yet).
On a side note, when the Reapers actually arrive, why do they immediately start targeting planets instead of throwing everything at the citadel. If all the Reapers went there together, could they not curbstomp the citadel fleet and shut down the relay network? It looks like that's what they did to Earth instead, only they (seemingly?) get far less of an advantage out of it. When the Alliance reclaimed the Normandy, did they immediately start mass manufacturing Reaper IFFs? (i.e. if the Reapers don't actually shut down the relay network, but just make it unresponsive to any non-Reaper ships, widespread use of Reaper IFFs would negate the advantage)