Some guy on gamefaq claims to know the original way Mass Effect 3 was suppose to play out. No idea if its true but I can tell you its way better then what we got.
After checking these boards, bioware forums, the twitters of various people involved with the game, audio file rips as well as some information I've gathered from other sources, I decided to talk with someone who used to run their own review website who still has ties to some people in the video game industry. That includes Bioware (they had sent him early review copies of the first ME). Anyway that's not what's important. The point is what I'm about to say you can take with a grain of salt if you want. I'm not here for attention or because I'm a fanboy of bioware. I'm simply here to help you all make sense of this situation. It will make a lot of sense and put the little things you've all found together. The reasoning for the ending change was they needed more time to implement it (this was supposed to be the reason for the delay) but Kinect implementation and the desire by some people (perhaps EA) to have an ending where things are left to interpretation messed with this. The ending was quickly altered which is why things don't "fit" and there are plot holes. Anyway, below is how things were supposed to happen.
The original ending was SUPPOSED to be extremely varied. Everything remained the same up until the part when Harbinger shoots at you and your team. This is when information that has appeared here already comes into play. There were going to be various outcomes determining how you reached the citadel and it was HOW you got there that determined what endings would be available to you. The following were the different scenarios from worst to best (based on EMS and war assets)
A: Your whole squad gets wiped out (the two crew members you took with you, Anderson). You struggle to make it to the citadel. Right as you're about to make it to the beam, Harbinger talks to you, saying you've been defeated and he kills you. Joker tries to swoop down to save you, but he also gets shot down.
B: Most of your squad gets wiped out. Still only you are able to make it to the citadel. Once up there, you must confront the illusive man alone. Because of this, unless you have high reputation and either talk him down or renegade interrupt and shoot him, he kills you and tries to control the reapers, but fails as he discovers he was indoctrinated.
C: You and Anderson make it up to the citadel together and make your way to the control panel where you confront TIM. The same thing plays out where you can talk him down. With high enough reputation, you can "save" Anderson but its not necessary for you to make it to the next part. Anderson dies after TIM is shot or kills himself like in the ending we got.
D: You and Anderson make it up to the citadel together while you're two squad maters, who clearly survive, are holding off the reapers from following you to the citadel. Everything continues the same here as "C" until after TIM is shot and killed and the final conversation that Anderson and Shepard have (which is much longer than what we got). You get the shorter convo in C.
[The following you only see with outcome "C' and "D"] Shepard looks out at the war going on and activates the crucible. Hacketts says its not working. This is when Harbinger talks to Shepard through TIM as he lies on the ground. Harbinger tries to convince you that you've fail but you can argue with him. Harbinger says that he has your crew in his cross hairs. We see the Normandy arrive (the joker dialogue that was cut) and the rest of your friends help the two squad members you brought with you face off against Harbinger and his reaper minions.
You basically have a choice. You can submit to him and he claims he will spare your squad and earth until the next cycle because he is impressed that you were able to make it this far. This is when the motive of the reapers is more clearly established. Harbinger reveals that in the previous cycle, the prothean empire became too vast and they began to control all the other races, which would have prevented all of our races from developing. However, through more discussion, Shepard can uncover their true motives. They fear that they will be rivaled by something more powerful than they are (that this cycle will create AI that can topple the reapers). This implies they are merely fearful for their own survival and that is why they purge all life but they convince themselves they are protecting us.
Either way, you can submit to him and save your people or take your chances. Having 4000 EMS, not submitting to him you would lose everyone, but still eventually get to the three choices we actually got (more on this in a second). Having 5000+ and depending on how you resolved conflicts between characters and races, certain people will live or die.
After rejecting him (whether you lose everyone or not), you end up in the area where vent boy was but hes not there. It's just you and "Harbinger". He explains that a new solution is needed. The solution he tries to convince you to take is merge (to perseve his kind). But if you have high enough reputation once again, you can open the control and destroy option. Harbinger tries to talk you out of it by discussing how your races are divided and mentioning the geth incident. You convince him otherwise, and it is at this point, the control option opens next where he admits that shepard may have a perspective he never considered. Harbinger tells Shepard that if he destroys them, the relays will be destroyed as will the geth (which is true. This is the only ending where the relays are destroyed).
Now for the four endings.
If you submit to him before the three main choices, the reapers leave earth but end up wiping out every other race who haven't proved themselves worthy. Shepard dies.
If you merge, the reapers leave and like the ending we got, we see all the characters we know with green eyes as a green light brightens the sky. Shepard dies for the same reasons in the ending we got.
The control option, the reapers leave. Everyone cautiously celebrates while joker and your LI look up to the sky and wonder what exactly happened. Life goes on but its hinted that the reaper threat may return. This ending ends on a cliffhanger.
The destroy ending does destroy the relays, but its implied that with all the races on earth, they, together, will restore what they lost and will attempt to work together. if shepard lives, your LI leading your squad, will be looking for you. You are beamed back down to earth (its assumed shepard was somehow blasted into the beam? this is the only questionable part). It ends with shepard's hand coming out of the rubble and breathing. Still a cliffhanger of sorts, but you can assume they will find him/her obviously.
Not sure if this is true but **** that would have been way better! Also, if this is true, then Bioware must have the unfinished assets and they should go finish the ****ing thing!!