This is a really, REALLY long post, but it covers everything regarding both the original ending that was scrapped pre-release and the current ending that shipped, so if you are interested in the details (and minor humor) then enjoy!
The ending ruined it for a lot of people...I've traced and covered just about every corner of the internet on this subject and the number one reason for this ending was because someone on the inside leaked the original ending online about a month before the game was set to ship. The heads at BioWare didn't take too kindly to this because they wanted everything about the game, especially the ending, to be hush-hush. So with that being said, lead writers Casey Hudson and Mac Walters locked themselves in a room and rewrote the entire ending, ensuring that now one other than themselves would know the conclusion until the game released.
In case anyone is interested, the original ending centered around the theme of dark energy which was greatly foreshadowed on in Mass Effect 2. By the end of Mass Effect 3 it would be revealed that the true purpose of the reapers was to delay as well as solve the problem of dark energy / dark matter. In other words, the reason for the 50,000 year cycles is because by that point, the galaxy's races have reached their high point and dark energy is being spread at alarming rates. Things like FTL, the mass relays, biotics, element zero, all helped accumulate dark energy.
As I said, the problem is foreshadowed upon in Mass Effect 2 when Tali is researching Haestrom's sun. The issue is that the abundance of dark energy is causing stars such as suns to go supernova billions of years in advance, and if the reapers did not intervene every 50,000 years and eliminate all sentient and advanced life, the problem would spread and the entire galaxy would end up going into a massive supernova. In short, it's a plot twist that explains the reapers are technically the "good guys" when looking at the larger picture, despite their horrible methods.
At this point, it was to be revealed the player that the cycles would not continue much longer as the reapers are running out of time to find a solution, meaning, the galaxy's destruction is imminent. However, the reason the reapers and the collectors focused on human abductions in ME2 (and the reason for the human reaper construction) was that humans had unique DNA that could work as a solution to the dark energy crisis. The only reason that the reapers targeted other species as well was to help stop the spread of dark matter and because they allied and took up arms with humans; keep in mind, they killed asari, krogans, turians, etc, but only processed humans.
Here, the player would be given two choices: Either destroy the reapers and take your chances as a galaxy united to figure out a solution to the pending doom, or end the war by sacrificing all of humanity to save the rest of the galaxy from destruction. In my mind, it was brilliant because not only is a difficult choice, they are both morally grey. Is this dark energy crisis true? Are we all going to be killed? Will sacrificing humans actually stop this? Is it right to sacrifice every man, woman, and child of the human race to save the galaxy? Are the reapers bluffing? Do we instead carry out our mission and destroy the reapers? And in doing so, can we actually stop this dark energy crisis? So many questions for two choices that would have a major impact on the galaxy moving forward.
Instead, we got red, green and blue...so because the lead writers didn't like the fact that this dark energy ending leaked, the reapers motives are killing us every 50,000 years because we build robots that are going to kill us, so their solution is to kill us so that we don't build robots that will kill us...even though most of us JUST BROKERED A PEACE BETWEEN THE QUARIANS AND THE GETH WHO WERE AT WAR FOR 300 YEARS. It's so stupid, irrationally, slopped together, and is full of so many plot holes:
- How is Shepard not incinerated by Harbinger's beam?
- Why does Harbinger just fly away...and worse, with the Extended Cut, why does Harbinger just watch casually as Shepard says goodbye and sends the Normandy off?
- After Shepard gets up, why is Coats ordering a full retreat? Umm, last I checked our ONLY HOPE was getting someone to that beam. Why throw in the towel, ESPECIALLY as Harbinger is LEAVING the beam, meaning, it's LEFT WIDE OPEN...
- How did Anderson follow Shepard up the beam, yet, end up ahead of him?
- Why were there hundreds of Ashley / Kaidan husks laying around?
- Where did the Illusive Man come from...? And how does he now have biotics?
- The rachni spoke of indoctrination as "oily shadows"...hmm, I noticed a bunch of those both in the dream scenes as well as on the Citadel after Harbinger's blast, especially during the scene with Anderson and the Illusive Man. Also, the codex talks of growls...there's plenty of those in that same scene.
- Oh, and speaking of growls, let's take a trip back to the very first mission with that kid in the air duct. How did Anderson, two feet away not hear that conversation and come over to help? Oh, and did you notice that there was a growl when the kid disappeared? I sure did.
- Speaking of the kid, when he runs to the shuttle, why does no one help him? There's bunch of soldiers and a shuttle full of adults just standing there...yet, Shepard somehow is the only one to see that kid? From the Normandy no less?
- Back to the ending, why is it that after the Illusive Man makes Shepard shoot Anderson that Shepard magically gets that same wound, and that the camera makes it a point to focus on that?
- And How did Hackett know someone made it to the Citadel? Didn't Coats say everyone was wiped out and that he was ordering a full retreat?
- What's up with this star child...reapers are killing us because if they don't kill us then we will build machines that will kill us, so if they kill us first we can live so that they can kill us again in 50,000 years before we build other machines to kill us......right.....ok then......
- If the Citadel is above Earth, then why when we see the crucible blast shooting throughout the galaxy does it begin in the Viper Nebula? Shouldn't it be originating from Earth? Well, according this scene, it somehow magically shoots off there instead and has to go through about five or six mass relay chains before it gets to our solar system...because that totally makes sense...
- With the Extended Cut, in the destroy ending especially, we see slides of London rebuilt, Rannoch as a thriving city, Tuchanka being rebuilding and krogan babies in arms. What does this mean? It means that this didn't happen overnight...so then why is Shepard not in any of these scenes...like did they just leave him sitting in that rubble? Did they decide that they didn't want to help, instead, they'll just leave him there and build a giant monument overtop of him? The hell?
- Speaking of that rubble, it looks a lot like London if you ask me because I see concrete and concrete buildings, none which were on the Citadel. So that means Shepard survived a giant explosion in his face, survived the entire core of the Citadel exploding around him, was shot into space, entered the Earth's atmosphere, somehow wasn't torched by that either, crash landed back down on London, and SOMEHOW by the grace of space magic, is alive, intact, and breathing.....HUH?!?!?!?!?!?!?!?
- So then let's play devils advocate for a moment and assume that this scene is still on the Citadel. That means he still survived the giant explosion in his face and can also breath in space because there is no life support systems on the Citadel at this time because the entire thing is wrecked....the slide of the Citadel shows this, it shows it in pieces and it shows that there are no lights, no power, no energy, nothing, just wreck and fallout. So Shepard breathes in space now...awesome, I love that space magic, gosh it's the darndest!
So yeah...that's just some plot holes to name a few.
And guess what? It can only be described in one way...
SPACE MAGIC!!!!!!!!