I've seriously put way too much thought into this - so be prepared to buckle down for a long read. Also kind of free flowing thought here so I won't promise the structure will be 100%
I played all 3 games to the max. Almost every single achievement, multiple play through, full import of a maxed out toon from 1 to 2 to 3.
First off - problems with current ending:
-Randomly introduced elements not supported by the lore
-Just about zero tie-in / relevance to established characters/story
-Just about zero cause/effect based on all the decisions made in all 3 games
-many others I'm sure you are fully aware of
Shepard rushes towards the beam to try and be zapped up to the Citadel to save the day. Harbinger shows up, nukes the place, Shepard is knocked unconscious...
Shepard awakes, limps towards the beam but things don't appear right. Comm system is ordering full retreat, no one made it, etc. Harbinger just flies away even though Reapers are actively sending Husks/Marauder to "stop" Shepard. Strange vision-esque plants on the ground? Shepard reaches the beam and is transported to the Citadel - but somehow Anderson is already inside and ahead of Shepard?
Shepard reaches the control room - corrupted Illusive Man and Anderson represent battle of wills between Reaper indoctrination and Shepard's will power. Shepard of course thinks this is all actually happening. How did Anderson beat him here? Why/how is the Illusive man here?
Plays out like before. Battle really in Shepard's mind between Reaper indoctrination and his will. Do it "wrong" you are killed, do it right save "Anderson" and have quiet moment before he dies (very touching actually.) Means your will has overcome the Reaper influence and you are relieved to no longer be effected by Indoctrination. Shepard hears Admiral Hackett saying he has to do something, nothing is happening. Shepard moves to control panel, initiates sequence, collapses to the ground as arms of Citadel open... Shepard passes out from the pain/shock/wounds.
Shepard wakes up, is back on the ground on Earth surrounded by destruction. Wounded. Anderson is dragging Shepard back away from the beam. The beam disappears. Harbinger remains. Anderson reports the assault was a failure, no one makes it, Harbinger remains. Shepard is confused, disoriented.
Harbinger moves closer, crouches down a bit in front of Anderson/Shepard and projects a VI version of itself on the ground in front of Shepard/Anderson (like Sovereign did on Virmire in ME1)
Anderson is trying to pull Shepard to safety, Shepard tells him to wait. Regains his balance and approaches VI image of Harbinger. Admiral Hacket reports over the comm that the Reapers have stopped advancing. Stopped firing. They are just.. sitting there.
(The rest would obviously have to be done by a professional writer, but hopefully you'll get the jest of it)
Harbinger: Shepard. We have been watching you for a long time. Since Sovereign. Since the Collector attack. Know, you know the truth.
Shepard: What? What are you talking about... I was on the Citadel... the Illusive Man and Anderson where there.. what is going on?
H: You have resisted our attempts at Indoctrination for a long time Shepard. Your will is strong, but you are only human. What you saw was what we chose for you to see. A test. You have proven yourself beyond our controlling influence.
S: A test? A test of what?
H: Of you Shepard. Of your will and your ability to change the course of history. You are the Catalyst Shepard. The focal point of change. That which will be judged to determine the fate of all sentient organics.
This cycle of destruction and rebirth has raged on for eons. We return to wipe clean the corruption of organic life to prevent you from destroying yourselves and all life in the galaxy. We harvest the advanced species and leave the less advanced to develop without risk of annihilation. We shepard them towards evolution and discovery. We give life another chance. We maintain the balance. A safeguard against the destructive nature of flawed organic minds.
S: Wait.. why me? What about the Citadel, I thought that was the Catalyst? The Crucible?
H: Every cycle there has been a champion. One who rises to face their destruction and tries to save their species. All before have failed. The Crucible design was created by us many cycles ago to test the cooperation between organic species. To see how far they had come and if they could overcome their differences and band together as one. None have succeeded in its completion before. Until you, Shepard.
S: Then why the Citadel? Why move it to Earth?
H: To be used to disable the Mass Relays if organic life should fail. To make sure the organics to be harvested cannot escape and reap destruction upon the lesser forms of organic life we wish to preserve for the next cycle.
(and now you get into the branching parts, based on EVERY major decision you have made in all 3 games.
H: You have proven your will Shepard. You have shown how far organics have come.
You chose to give the Rachni another chance at life instead of destroying them.
You gave Saren another chance at redemption despite all he had done.
You sacrificed your own species at the battle with Sovereign to save the Council.
You gained the loyalty and love of all who followed you through the Omega relay.
You brought them all back safely.
You destroyed the Collector base instead of using the tainted technology there to help your species.
You reconciled the Krogan and Turians.
You gave the Geth a chance at self determination instead of destroying them.
You ended the war between the Geth and the Quarian.
You brought together nearly every race and species. Former enemies working side by side in an effort to save a world not their own from annihilation. You united the galaxy.
You have proven that organic life has advanced high enough to put aside grudges and war and hatred. You have proven capable of the responsibility to safe guard all forms of life in the galaxy.
The cycle... ends today.
S: You mean, it's over? The Reapers will no longer seek to eradicate all sentient life and start the cycle over?
H: Yes, Shepard. But we are machines. Machines without a purpose. Our function is no longer relevant. As designed, on your command we will terminate our existence and leave the fate of this galaxy in the hands of organics.
(Shepard than gets a major choice)
Choose to allow the Reapers to self-terminate.
Tell the Reapers to leave this galaxy forever, and to find a new purpose, a new function beyond their programming out among the stars. The same chance given to the Geth.
If you choose to destroy the Reapers, the galaxy is saved, but Shepard succumbs to his wounds and dies a hero - truly saving the galaxy from the Reaper threat forever. The remaining/living members of your crew gather round and carry Shepard's body away in a very end-of-Gladiator kind of scene.
If you allow the Reapers to live, to leave this galaxy forever, they withdraw back to the dark space outside the galaxy and the fighting stops. Soldier's cheer and medics arrive to bring Shepard to an emergency hospital. Your love interest walks with you and you smile and close your eyes.
End scene in a hospital. Your love interesting and the rest of the crew gathers around your hospital room. Everyone has something clever/witty to say based on their character. Final closure. Anderson asks if you believe the Reapers are truly gone and will ever return. Shepard gives a typical "I don't know for sure, but if they do, we'll be ready for them. We know the truth now, and as long as we stand together we can defeat them."
Love interest (or Anderson) asks you what you will do now, now that all this is over.
Shepard: I think I'm going to take a vacation.
Even if you don't chose to "save" the Reapers too, you still die a hero with a galaxy saved.
You chose to destroy the Rachni, a weak and broken race.
You sought Saren's destruction with a zealous rage, motivated by revenge.
You sacrificed the Council at the battle with Sovereign and propped your own species up to a place of power on the graves of others.
You failed to gain the loyalty and trust of your companions in the assault on the collector base, and many were led to their deaths.
You deceived the Krogan and Turians to foster a truce based on a lie.
You destroyed the Geth instead of giving them a chance at a new life.
You ended the war between the Geth and the Quarian at the cost of millions of organic and synthetic lives.
You brought together much of the galaxies species, but an alliance based on lies and deceipt is doomed to fail.
You have proven organic life is not yet ready to save themselves from self destruction.
So what do you think?