Okay, here is my idea about how the ending should have been, or how it could still be, since it incorporates the indoctrination theory. It was inspired by several things I've read, heard, watch online (most notably this guys videos), so I'm not claiming that it's 100% original or anything.
So let's follow the indoctrination theory line (even though I would rather change the Earth battles into a Siege of Denerim type of battle from Dragon Age Origins), Shepard successfully fights indoctrination, and wakes up to one of her (I will keep using the female pronounce, cos I play FemShep) squad mates and Anderson trying to wake her up. Your other squad mate either died or gets knocked out (not sure about what kind of mechanic to you to determine this, maybe a ranking of the squad mates like for the suicide mission in ME2, where a low health character could die, but if you helped him/her resolve his/her problems, then he/she only gets knocked out...or something).
Once Shepard is awake, they find cover somewhere. Harbinger is gone, but so is the beam leading up to the Citadel. Shepard contacts EDI, and asks her to scan for a possible way to enter the Citadel. She finds a hull breach that could work if they fly there in a shuttle.
[If Cortez is alive] Steve will contact Shepard, and tell her that he tried to fixed the shuttle and it is operational, so with its stealth drive, they can do a likely successful drop onto the Citadel. Which is what they do: you, Anderson and your squad mate land on the Citadel.
[If Cortez is dead] You get a shuttle from the ground team with a random pilot, but since the shuttle doesn't have a stealth drive, you get shot and have to crash land on the Citadel. Your pilot and your squad mate both die.
In both cases Admiral Hackett and the fleet provides a distraction so Shepard and the other will be able to make the landing.
Once on the Citadel, you have to make your way to the Council Chambers, since it was established in ME1 that that's where the controls to open the Citadels arms are. You have to fight several Reaper ground forces on the way.
[If your Citadel Defense Force score is very low] You only find dead bodies everywhere.
[If your CDF score is low and your squad mate is alive] You find a somewhat injured Commander Bailey, who fills you in on what happened, and offers assistance (more on that later).
[If your CDF score is low and your squad mate is dead] You find a somewhat injured Bailey, who fills you in on what happened, and becomes a temporary squad mate for the rest of the game.
[If your CDF score is medium] You find a couple of refugees protected by a very small team of C-Sec forces. Commander Bailey is alive, fills you in on what happened and offers assistance even if it means abandoning the refugees.
1. You can tell Bailey to abandon the refugees and help you get to the tower. (Renegade) 2. [If Cortez is alive] You can order Bailey to escort the refugees to the shuttle, which will take them away from here.(Paragon, increased enemy forces later on.) 3. [If Cortez is dead] You can tell Bailey to focus on protecting the refugees. (Increased enemy forces later on.)
[If your CDF score is high] You find more refugees and C-Sec has enough power to stand their ground against the reaper forces. Doc Mitchell (or Chakwas, or some other doctor) and Commander Bailey are alive, and they have enough forces and resources to provide you assistance and protect the refugees at the same time.
Once again, your make your way to the Presidium and the tower.
[If you have Bailey (and C-Sec forces) aiding you] Bailey diverts reaper ground forces, making Shepard's fight easier.
[If Bailey is dead or your squad mate] Increased combat difficulty with more ground forces. You reach the base of the tower, but more reaper forces are coming.
[If your squad mate is alive] He/she stays at the bottom of the tower to hold the enemy off, while Anderson and Shepard go up the tower.
[If squad mate is dead] Increased enemy forces later on.
You make it to the Council Chamber, where you find the Illusive Man, who similar to the previous “dream” about him, is indoctrinated and has implants like Saren did.
You have a conversation with him about how he still wants the best for humanity and controlling the reapers is the best etc. You have the options of talk him down, like with Saren, in which case he kills himself, or if you fail that you can keep him talking and wait for a Renegade interrupt, which would result in you killing him. If you fail that too, then he reaches his final state of indoctrination and becomes a boss fight. (Obviously this is just a very basic breakdown of what could happen, since I didn't really feel like writing out a whole dialogue tree.)
Either way, TIM is dead. Shepard steps up to the console while Anderson covers for her killing some husks. While Shepard operates the console a hologram of Harbinger comes up, and starts talking. You have the chance to ask him about various things, but Harbinger sort of answers in the same manner Sovereign did, and doesn't really tell you anything useful. You have the chance to voice the wish for co-existence (Paragon), or just tell him to go to hell (Renegade). Harbinger says that even with the Crucible you won't succeed, and disappears.
The Citadel's arms open up, the Crucible docs, and it turns out that it is something similar to a Thanix cannon. Basically it's a giant gun that can kill reapers, but still needs to be targeted at them and doesn't uses the Mass Relays fro spreading it. You sync the Citadel's systems to the Normandy, so EDI can target the reapers.
[If you have low EMS] The Crucible doesn't dock properly, and while trying to fire it, it blows up itself and the Citadel too. Shepard and everyone on the Citadel dies, the Victory fleet gets destroyed, reapers win and harvest everyone.
[If you have medium EMS] The Crucible fires, kills several reapers. Harbinger starts to move in on the Crucible. Hackett orders the fleet to protect the Crucible no matter what. After some devastating space battles, Harbinger manages to destroy the base of the Crucible (and the Council Chamber with it, more on that later). However there are only a couple of reapers alive with Harbinger, the Victory fleet attacks them with their remaining strength and manage to kill them, but the fleet itself is also almost completely gone
[If you have high EMS] Same as above, but the only reaper left alive is Harbinger. The Victory fleet defeats Harbinger, and while they suffer some casualties, the bulk of the fleet is alright.
Meanwhile what happens to Shepard and Anderson on the Citadel:
[If only Bailey is alive] You get him on the radio and listen to him giving you a last warning about more forces coming, then he dies.
[If Bailey and C-Sec protected the refugees and Cortez is alive] Corzet contacts you that the refugees and Bailey are on board, and they will make it to Earth.
[If Bailey and C-Sec protected the refugees and Cortez is dead] Bailey contacts you, but you mostly hear static. Bailey and the other are dead.
[If Bailey, some C-Sec guards were aiding you and your squad mate is alive] Only Bailey survives and promises to fall back to aid your squad mate, still there will be less enemy forces later on for Shepard to deal with.
[If Bailey, several C-Sec guards and your squad mate are alive] They cleared the area and promise to rejoin your squad mate at the bottom of the tower as soon as they can.
[If your squad mate is dead, but Bailey is alive with several C-Sec guards] Bailey tells you that they will try to fall back to your position, so that you could escape. Since no one is protecting the tower at the time Anderson and Shepard have to fight.
[If Bailey is your squad mate] Bailey tells you that many reaper forces are coming, but he will try to hold them off. He fails and dies. Anderson and Shepard have to fight the rest of the enemy forces.
[If your squad mate is alive, and Bailey was dead] He/she radios in that there are an overwhelming force of enemies, but he/she will try to hold the line. Eventually he/she dies, the reapers make it to the Council Chambers, Shepard and Anderson has to fight them.
[If your squad mate is alive, and Bailey (with C-Sec) died] He/she tells you that he/she can't defend the tower bottom from both sides, so he/she will choose a side to fall back to, and the Shepard has to deal with forces from the other side making their way up.
[If your squad mate is alive, and Bailey is alive too] He/she reports that while there is still enemy presence there, it's not that bad, and you can come down safely.
If you have to fight reaper forces in the chamber, that happens before Harbinger destroys it and the Crucible. Anderson (and possibly Shepard too, depending on how many forces you got to fight) gets wounded in the fight, and try to limp to the way back. They have some dialogue about “We did it!”, and “I was always proud of you child.” etc. Harbinger's beam destroys part of the chamber that collapses on Anderson and Shepard.
[If your squad mate is dead] Both Shepard and Anderson die.
[If your squad mate is dead but Bailey and several C-Sec guards are alive] Bailey and the guards make it to the bottom of the tower with minimal casualties. Some guards stand their ground down there, while Bailey and some of his men go up to the chambers. They get Shepard out of the rubble, and hurry back to the hospital, but don't make it in time. Both Shepard and Anderson die.
[If your squad mate is alive, and Bailey died] Your squad mate makes it up to the chamber, but can't get you out under the rubble by him/herself. Both Shepard and Anderson die.
[If your squad mate and Bailey are alive] Bailey eventually manages to join up with your squad mate, and they both make it up to the chamber, and while they can get Shepard out of the rubble, they have no means to save Shepard's life (since the refugees and doctors are all dead). Both Shepard and Anderson die.
[If your squad mate, Bailey, and several C-Sec guards are alive] Since the area is clean C-Sec is free to move, they join up with your squad mate, radio to the doctor's to get to the tower bottom, to help the injured. Your squad mate, Bailey and some C-Sec guard make their way up to the Council Chambers, where they find Shepard, quickly radio a doctor to come, and manage to get Shepard out of the rubble in time, and save her life (though she will still need surgery and several month to recover).
[Bonus ending, if you made peace between all races, have very high EMS] (not sure if it should be included, but why not) Similar to the above, only they manage to save both you and Anderson.
Then depending on which ending you get, you have varied cut scenes about either soldiers cheering or reapers killing everyone. If you manage to defeat the reapers, you get a written (possibly narrated) epilogue with some art in the background about what happens to the galaxy later on. I'm not going into detail with this, because there are so many variables, that it would take forever to list them all.
I feel that this kind of ending is similar to the suicide mission, and would make more sense for the game, since the conversations you have on the Citadel would actually matter. And you still get a “bittersweet” ending most of the time, where Shepard dies, but if you really work hard for it then Shepard can live, because I think if you do plan all your games carefully (don't kill Wrex, have Thane live etc.), the player deserves the chance for a “happy” ending. But even the “happy” ending can actually pretty much suck, because if you only got the Citadel Defense Force at full strength, the fleet you gathered will still die.
Also I left the Reaper's reason out on purpose. I personally feel that they didn't really need one, and actually keeping us in the dark about that would have been a positive kind of speculation, which is what Walters wanted, if you can believe his notes. It would also present a really great opportunity for a new game where Shepard isn't the hero anymore, and which would revolve around finding out the actually reason for the Reaper's harvest, which could be something like that dark energy problem Drew came up with and which was hinted at a lot in ME2, and suddenly you would have a new galaxy threatening problem that needs to be solved.
PS.: Sorry for any grammar problems, English is my third language so I'm not nearly as good at it as I could be :D
Edit: Added a player choice, where Shepard can tell Bailey to either protect the refugees, or help Shepard.