Mass Effect 3 Ending Controversy - SPOILERS

It has been less than 2 weeks since the release of Mass Effect 3, a fan favourite series where you play the hero, Command Sheppard, out to save the galaxy from the threat of extinction by intelligent machines called Reapers. The Mass Effect series is notable for allowing players the maximum choice ever seen in this type of game. The choices players made in the first two Mass Effect games carry over to Mass Effect 3 and affect the story. 

Or at least this is what players were led to believe.

Are there alternative endings depending on what you do in the game?

It's not so much that there is a fixed set of alternative endings, but all of your choices really determine how things end up in the universe. So, how you approach the end-game, for every player, you're going to have a different set of results in terms of who is alive and who is dead, and which civilisations survived and which ones were wiped out.

Facebook, twitter and the ME3 Bioware Forums have been boiling with fan dissatisfaction regarding the ending of Mass Effect 3, billed as the end of the series. There are reports that a fan has lodged a complaint to the FTC. A Bioware forum poll has 91% wanting an ending change.

Do the critics have a point? Here are a few from the "sucks" side:

Article - 5 Reasons The Fans Are Right
Angry Joe Video - 10 Reasons We Hate Mass Effect 3's Ending 

And a don't be a whiner counter opinion from IGN.

Like or hate the ending, there are huge plot holes in the last 10 minutes of the game. I mean big ones. 

Even as I was playing the ending sequence, I suspected that it was all a dream. The lack of logic, especially from the "starchild" was too obvious to miss. In fact, this would be an awesome false ending, assuming that the present ending was an indoctrination attempt and only by choosing the "red" or destroy option, you would be allowed to actually carry on the fight to the Reapers. This is being called the indoctrination theory on the forums and is the only way I can see to explain the huge plot holes and logical inconsistencies in the statements by the "starchild". 

Here is an excellent discussion of the Indoctrination Theory. 
Update: And this Indoctrination Theory video is even better. 
Update: Angry Joe has an Indoctrination Theory video as well. This is also good and has some aspects about indoc theory that I missed.

The only thing that makes this ending make sense is that Bioware set up this false ending and there is still a piece of the game, the real ending, that they will release as DLC. I am not sure why they would do this. There was a large outcry with the release day DLC From Ashes, I cannot imagine why they would take out the ending for the game and release it later, unless it was the biggest joke played on gamers ever, or someone lost a bet. 

The only other assumption is that the writers really suck that bad. But the writing for ME 1 &2 is good, arguably some of the best in video games. ME3 writing is also good throughout the game, until the final 10 minutes. I greatly enjoyed ME 3 The writers did a great job of building up the tension towards the ending. I wasn't sure how it was going to end but, as Sheppard, I was ready to make the ultimate sacrifice, for the good of the galaxy. 

I wasn't prepared for what I got. This tweet sums it up.

Is there more in store? Check out this tweet.

Or this rumour that came out a few days ago. Treat this with a big grain of salt.