Note: This is obviously full of spoilers. So don't read it unless you want the game ruined for you.
I am not the author of this idea, either. This was posted on Reddit by user 'Axewerfer.' And I think it's brilliant. Simply reading this gave me better closure than ME3's actual ending did. Too bad this guy doesn't work for Bioware.
So here it goes...
Things progress as before, learning that the Crucible needs the Catalyst, proceeding through the Cerberus plans and plots, learning that the Citadel is the Catalyst, and onward to Earth. Once at the beam, however, things change drastically. Again, Harbringer descends and destroys the troops, only this time Shepard does not reach the beam. Harbringer stops to directly address him for the first time, ignoring the incoming fire from the assembled fleet. Perhaps Shepards squad members survive, perhaps they don't. At this point, it is a futile gesture. Harbringer has won, and it knows it. Harbringer tells Shepard that the cycle must not be stopped, hinting again that the Reapers are driven by something greater than their own motivations, and reiterating the Rannoch-reapers statement that the Reapers are the only hope for sentient organics. Interestingly, for the first time, Harbringer indicates that they, as much as anyone else, are victims of this cycle. Crucially, it must become obvious at this point that the Reapers, while incredibly advanced, show no sign of altruism or nobility, and do not have the capacity for self-sacrifice. As such, they are not sentient.
To reiterate, the Reapers are less developed than the Geth or EDI. They are an evolutionary dead-end, as Synthetic Lifeforms go.
This fact should be immediately realized by the Geth (if they still exist) and EDI. What follows should depend on the players actions in the previous games and ME3. Whatever happens, people, ships, and old allies begin fighting to protect Shepard. They hit the Reaper in it's main 'eye' as it prepares to fire, distracting Harbringer, and buying time for Shepard to crawl the rest of the way to the beam. Perhaps nobody is left. Shepard dies. It's a sad ending, but a noble death, facing down a 2 mile high monster with your honor intact. Liaras time capsules survive, though, giving the next cycle a chance. But let's say Shepard makes it to the beam. Harbringer brings down the teleporter as he goes, leaving him alone. No Anderson, no squad, just Shepard making his way through the ruins of the Presidium. There are no survivors. As he reaches the awaiting Crucible, he is stopped by the most unlikely of figures.
No magical ghost child. In fact, the child could probably be removed in its entirety without hurting the game. The Catalyst is the Citadel, itself a small part of a much larger system. It has co-opted AVINA to speak with Shepard. As the battle rages on outside, Shepard and the hologram speak, as it takes on various forms of people he has met and seen killed. The VI is nigh-omniscient, with each rising galactic culture building the convenient Citadel systems into the heart of their communication and economic systems. The Catalyst has always been there, acting as a translator and silent observer, preserving a record of every species that has ever existed in the cycles. It is not a true AI, but the sheer volume of data is has available ensures that its primary directive can account for every eventuality. What that directive is does not need to be stated. As the Reapers noted, their goals are unknowable. Claiming that midichlorians cause the Force did not improve Star Wars.
However, despite all of its data, the VI cannot account for Shepard. It has no means of preventing him from using the Prothean Crucible, and instead, serving its enigmatic creators, offers him his choices on how to use it.
Option 1: The original intent of the Crucible, as a scorched Earth solution. The device will permanently render all Eezo in the galaxy inert. Starship cores will be lumps of useless metal, biotics will lose their powers, and the galaxy will be plunged into a dark age, free from the Reapers, all Mass Effect technology, and the Mass Relays. The fight will end, the fleet will fall silent. Earth is now the last refuge of a dozen species.
Option 2: Prompted by the arrival of The Illusive Man, a modified Crucible signal can control the Reapers and all other Synthetic technology, bringing it all under the sway of Organic life. The Geth, The Reapers, and EDI are all shackled AIs once more.
Option 3: Destroy the Citadel, free the Reapers. Shepard sacrifices himself, detonating the Crucible, destroying the Citadel, and the VI controlling the Reapers. Humanities greatest enemy is now an unshackled AI, free to self-modify their code, and find their own way in the universe. The Reapers stop their attack, and retreat for parts unknown.
Option 4: Do Nothing. Honor before death, Shepard disables the Illusive Man and sits, watching the fight with AVINA. With enough raw military strength, and the combined might of every fleet and empire in the galaxy, perhaps the Reapers might be defeated. Best case, the Reapers are destroyed outright, but at a terrible cost. Worst case, the fleet is swept aside and the Reapers are unchallenged. Middle of the road, the Reapers are slowed, for a time. Long enough to seed Liaras time capsules among the stars, and place members of each race into stasis pods as hope for the future.
Option 5: Well, maybe not. You remember what I set about EDI having the Capacity for Self-Sacrifice? Perhaps, if Shepard has made just the right choices through the trilogy, there is another way. The Normandy arrives, and EDI can transfer to the Citadel computers, displacing the Catalyst, and becoming it. There is a catch, of course. EDI has self-modified her code, and she has learned from Shepard.
a. EDI sends the Reapers away, giving the people of the galaxy another 50,000 years to rebuild and prepare.
b. EDI infects the Reaper code…with the Geth. The Geth take over the Reaper forces, becoming like unto gods. The outcome depends on Shepards interaction with the Geth up to this point.
c. (If Shepard chooses a Paragon path when dealing with EDI) EDI sacrifices herself, transferring herself to the Reaper ships like a virus, and disabling them from within. With their Kinetic barriers down, the Reaper ships are annihilated by the fleet.
d. (If Shepard chooses a Renegade path when dealing with EDI) EDI's self-preservation instinct is fully intact. She still destroys the Reaper ships, but she does it from afar, ensuring the the two fleets are evenly matched. The destruction is total on both sides.
The ending shows each of the companions. If Shepard is alive, with a conversation, if they're dead, as a cutscene. Party members killed in action are added to the memorial wall, which the camera slowly pans down, showing each of their faces as the name passes by.