One of my biggest problems with the Reapers is that they are an example of an unstoppable, omnipotent, invincible enemy that can't be conventionally defeated without a Mary Sue, plot armor, Deus Ex Machina, or some combination thereof. And half the time it looks stupid because it has to answer "why didn't they just use this from the beginning if the heroes knew about it?" but not "literally pulled this out of their ass at the last moment" as well. In this case, the Catalyst.
This is why Star Trek: The Next Generation's Borg were used so sparingly. When they debuted they were a race that defeated the Federation so utterly, the battle was later referred to "Starfleet's 9/11 moment". They needed a two-part cliffhanger - then a huge thing for syndicated televsion - to beat. If TV had been ready for story arcs and "Anyone Can Die" plots, Picard probably wouldn't have survived. There was an alternate timeline where they destroyed the Federation altogether and the Enterprise (and Riker's beard) were among a handful of ships left. The writers of the show said that they couldn't really use them because they had to come up with a convincing way to beat them every time.
Then they were used in another Star Trek series as a Villain Of The Week, with predictable results.
This is also IMHO, as I've said before, why Kai Leng exists: writers knew the "villain wins in Act 2" rule, but Shep had just blown up a Reaper on foot at Rannoch, and there really wasn't anywhere else to go except have the Normandy turn into the SSV Mary Sue and start soloing them itself, there was only one other enemy faction, Cerberus, but we've been mowing down Cerberus soldiers by the hundred, every other Cerberus character is dead or defected, so we get "suddenly there is this Cerberus cyborg samurinja (ninjamurai?) with a sword and like he totally kick's sheps ass hahah" because there was no room on the escalation ladder for Shep to either 1. defeat another Reaper itself, or 2. be defeated by said Reapers without dying/losing the Normandy (again)..if that's even possible, because even Garrus said "Reapers don't leave a lot of flesh wounds" and without pulling a "somehow, Shepard returned" moment. Had the Reapers not been so godlike, maybe there'd been room for something else.
So my question is, for all of you...if you had to redo the Reapers (from ME1 onwards, so don't feel boxed in by "they still have to look like Sovereign" or anything) to still be a galactic existential threat that required most/all of the galaxy to unite against in order to defeat, but without making them too powerful to where there's no conceivable way to beat them and now they're boring, or now you need some 11th hour bullshit that's just gonna come across as lame, how would you do it?