Here's the prevailing theory for ME3's ending as I understand it. This is one fool's take on events he has nothing to do with, so take it as you will.
1) The ME trilogy was originally designed based off a blueprint created by one guy: Drew Karpyshyn.
2) For unknown reasons, Karpyshyn was shifted to the Star Wars: The Old Republic project instead. Then he left the company completely.
3) ME3 had a good ending that was consistent with the original two games, called the "Dark Energy" ending. Short version of it is that the Mass Effect has a brutal environmental side effect (black holes and solar decay), and the Reapers are using the cycle to both limit its impact and create more Reapers in the hopes of brainstorming a more permanent solution. Harbinger would have believed a human Reaper would have been the ultimate resource for to that end.
4) Microsoft got stupid and released a demo of the multiplayer before they'd properly cleaned the code. People hacked the demo and pulled out the script, or at least enough of it to royally spoil the conclusion to about a decade of really hard work.
5) The team leads (minus Karpyshyn) attempted to write a new ending. Since the leak occurred very late in the development cycle, they didn't have much time and they were paranoid of leaks. They worked alone, to limit the risk of leaks, and completed it using as few outside resources as possible (only the kid and both Shepards were needed for voice acting).
6) Because it was written in isolation and in a hurry, the ending did not go through any sufficient critical review process. It was rushed out not only to meet the projected release date, but also to minimize the risk of spoilers. As such, nobody had the time or opportunity to say "this is stupid" or "this makes no sense" or "but this and this imply some pretty bad stuff".
7) It came out, and got the reception it did. For the first couple weeks, Bioware was under strict orders not to talk about the spoilers, so all they were able to actually do was act hurt and tease the "wonderful" DLCs they had been working on since it went gold but could not actually talk about either.
8) Bioware released the Extended Cut, which takes the abomination of an ending and polishes it until it's merely mediocre, possibly even a bit epic. The outrage is quelled and some good will is restored. Hard feelings remain and resentment continues, but in a relatively subdued manner.
9) We are here. ME3's first post-release, paid, content-based DLC is arriving fast. Will public interest and good will carry the DLC to profitability? Or will Bioware's rep be so tarnished that even the DLC for a genuinely awesome game (with a decidedly mediocre conclusion) will be received with suspicion? I honestly don't know.
Also, don't take that poll as gospel. It's an internet poll, and as such voting multiple times is not unheard of. If anything, it could be used to gauge the depth of passion in the response, if not the actual numbers.