Good article.
I would like to add a couple of extra examples (we need more? Yup. This ending was wrong on so many levels it is nearly incomprehensible that nobody at Bioware stood up and said "you know what, this makes no f@&*ing sense" before it was released), in LOTR terms because it's fun, the ending just did not work:
Suddenly, a plot element is introduced and the user told that this is what the game is about, when it clearly was not. Imagine at the end, Gandalf rides into Mount Doom and lectured Frodo that we should not judge people for getting addicted to the Ring, and his quest should have taught him this. Frodo says "I know, that's why I didn't kill Gollum straight away when I met him, and look, he turned out to be useful!". Gandalf tells Frodo to shut up and listen to his wisdom.
This is how I felt when suddenly, I was told that Mass Effect was about organics vs synthetic. It was not. This was one of many themes, one that I thought I had already concluded by bringing together the Quarians and Geth, and helping EDI develop a human personality. So, what happened to the themes of sacrifice, coming together to defeat all odds, and co-operation over war? Nah, they were all just minor issues. The real moral of the story is machines=bad.
The other is the old Deus Ex Machina. There are examples where this plot device can work, but they are very few and far between. Most story tellers regard them with the contempt they deserve. So, Frodo is standing over the Crack of Doom holding out the ring, having an immense internal struggle, when suddenly an orc walks up to him, stabs Gollum who is sneaking up behind him, takes the ring out of Frodo's hand and throws it into the lava. The Orc turns to Frodo and offers "we hate our existence" as a means of explanation, before offering Frodo an ice cream (in strawberry, mint or blueberry flavour, this is an RPG after all!) and walking off. Frodo just stands staring at the space this unknown character occupied for such a short time, and the reader throws his book at the wall shouting "what the hell!?"
The introduction of a hitherto unknown character to solve a weighty problem serves only to diminish the implications of the problem, not enhance them. The Starchild (seriously, if there are any writers out there, if you have a character named "Starchild" your story needs work) suddenly expects us to understand his motivations despite them being introduced out of nowhere. There is no option for Shepard to even question the Starchild, you just choose your explosion colour. Why can't Shepard tell the Starchild to stuff it? Why can't Shepard say "you know what, I have a pretty big fleet here, I'll take my chances". We are railroaded into accepting, without question, this brand new introduction to the story and it does not work.
If Bioware want Mass Effect to take the place it rightly deserves as the Paragon (ho ho) of Video Games, this ending needs to be fixed. Bioware is possibly the most interactive game company out there: senior staff members speak with the fans on a frequent basis to throw around ideas for stories, concepts and mechanics. It is not unheard of to change endings based on fan feedback, from Sherlock Holmes over 100 years ago to Fallout 3 more recently, and Bioware need to give this masterpiece the ending it deserves.