There is a "slow reaper progress condundrum". When I watched "War of the Worlds" (the remake by Steven Spielberg) I wondered why the Martians didn't use any kind of weapon of mass destruction. I think the answer is that Wells wrote the story before WWI, when the very concept was unknown and, it would seem, inconceivable. That's the way the reapers operate, too. It would be believable if they tried to harvest each species, but AFAIK they only try to harvest humans.
I'm not sure that giving them a weak spot is an idea that helps to solve that conundrum. There is still the reaper's inability to come up with convincing battle strategies and tactics (I'll give you two "likes" if you don't mention the "It's not about strategy or tactics" speech
). Then there is the question of why the reapers would allow civilizations to develop the necessary technology to become a serious threat to them, well beyond the stage where said civilizations could create AI's and synthetics that could wipe out all live in the galaxy, for that matter.
Well the only reason we have is that they somehow hoped the the civilizations would have the ability to not make synthetics that would rebel against them (despite the fact that they state that it's inevitable and that the organics will always follow the paths they make)... Ugh. I think the issue with the strategy and tactics is that Bioware themselves aren't familiar with strategy or tactics.
Alright, it is better to copy an old but good idea than to come up with something new that doesn' work
. So how would you do it?
Me personally? I'm a fan of having both be an option, so hear me out on this one because it's a bit wild.
ME1: Leave it. The plot has problems, but the general structure and ideas for it are okay. I might change things like have Miranda make an appearance in an attempt to rally support for Cerberus, and show certain figures (perhaps someone on a sidequest that you helped, join up with her).
ME2: ME2's plot should be... ME3's plot sans the reapers being there. One of my biggest problems with ME3 is that the timing for everything just feels wrong. All of these people rush off to go do their own thing when the reapers are knocking at the door. It just seems odd and kind of forced for drama TBH. So what we want to do is not have ME2 be pointless and more specifically, to give Sheperd something to do during ME3. So let's make ME2 to have just been "prepare for the reapers." Have all of the conflicts that rise up in ME3 be handled in ME2. Genophage? ME2. Geth versus Quarians? ME2. Asari problems? ME2. Seriously, just make ME2 literally about preparing for the reapers. You can even still have the collectors be the "main" enemy here to still give the reapers some "presence" as they make their way from dark space. It could also be used for foreshadowing to show that this is what they do to fallen organics and reveal that the reapers don't outright KILL the organics, but do *something* with them.
And then later on the collector base assault, reveal that not only do they turn them into foot soldiers like the collectors, but they make them into reapers. IE, why human colonies were being attacked. It's revealed that human colonies were chosen because a human, Sheperd, foiled Sovereign's plans, so human harvesting was used as a distraction for Sheperd while they continue to advance.
ME3: Assuming you have a certain amount of assets, Sheperd can stand together and actually defeat the reapers through a conventional victory because rather than spending the time of rallying everyone together, they can concentrate on actually finding and exploiting weaknesses against their foe. The crucible is still there in case you make mistakes, but it's not necessary in this version, and you can still win without it.
If you don't have enough assets to actually win, then there's the crucible, but it's more of a group of architects saying "guys, there's this thing we found that MIGHT help, but we don't know what it is, if you guys can hold the fort, we might be able to make this super thing that can win." So kinda like ME3 now except without the let's help everyone. Instead, the missions are more sidequest like than anything else and trying to hold the reapers back while the crucible is built.
Basically, I would have had ME3 go wild with any of the decisions you made. For instance, if you faked the cure of the genophage and Wrex was there, he would have the krogan troops fight against you because you left his people to die anyways, so he's going to make sure you don't live. Stuff like that.
My solution to this would be to have Shepard fail on more occasions. The player should not expect to win every fight, unscathed, neither should Shepard.
A good starting point would be to rearrange some plot points as they were planned initially:
1. Shepard looses the fight for Vendetta on Thessia against Cerberus,
2. The Cerberus coup on the citadel happens after that, the reason for the coup is that TIM needs to aquire the catalyst,
3. Shepard may be able to save the council, but shortly after that the reapers arrive and take over the citadel, so Shepard fails here, too.
It is not hard to turn ME:3 into an uphill battle that makes both Shepard and the player wonder if victory is possible, not by telling ("Our plan is oh so desperate, but we always win nevertheless, right?"), but by showing. Oh, and of course it should turn out that victory is indeed not possible, if the EMS is too low.
This is one of many surprising decisions that the BioWare team made about the ending. The crucible is always built, the beam run is always successful, the crucible is always docked at the citadel, it always "changes" the catalyst in a way that there is always a kind of "we win" - button.
Sounds like you and I are kinda on similar pages to just allow things to be pretty radically different. I mean, it's the end of the series. There's no reason to not have the game go absolutely nuts at that point.