So, their errors:
1 - Lack of villain agency (covered in my friend's blog post).
2 - Not following through on their promise to the audience.
3 - Expository finale.
Point one is covered quite nicely in my friend's blog post. When you pull back the curtain in the finale to reveal 'the true evil' (and the story isn't a mystery), then you're just sapping the villain's agency. This is a poorly executed reversal, the kind you don't want.
Point two joins hands with point one. In every story, the author makes a promise to the audience about the ending. There'll be some kind of emotional payoff. The hero may not fulfill that promise in a way the audience expects, but the promise is inherent in the conflict, often implied by the genre.
AVENGERS, for instance, promises us that the team will come together to beat the bad guys (it's a comic book movie). Any SHERLOCK episode promises that Holmes will use his crazy deductive skills to surprise us with the big reveal (it's a mystery, and despite being hit-or-miss they still try). Seriously, pick any genre and tell me what kind of story you can expect.
Mass Effect is a space opera summer action flick. What's our ending supposed to be? Space battle. Running gun battle. Big win to the conquering hero. I still expect sacrifice, preferably painful sacrifice, and, yeah, Shepard should probably die. That's not the problem. What did we actually get? Some vague swipe at wanting to be 2001: A SPACE ODYSSEY, or whatever the hell that was supposed to be, as read to us by the glowing Star Child thingy.
Which leads to my final point: expository finale, which Joe Abercrombie put quite succinctly: "Heavy exposition by a glowing child never before mentioned seems a sure sign of failure. By the time you get to the end of a hundred and fifty hours of gameplay, you shouldn't need things explained. You shouldn't be watching with furrowed brow thinking wha? You shouldn't be thinking at all. You should be feeling it." He makes a great point.
If you find yourself explaining every intricacy of your plot in a bit of summarizing dialog, you should probably bust up that dialog and put those plot elements into the story. Worst case, if you still need the exposition, we should think 'ohhhh!' and finally realize how it all makes sense. We shouldn't be going 'wait, what?' as the new data screws up the previous plot elements. That's what happens with a crappy reveal/reversal. A good one makes you see everything in a new light, and makes total sense. Think Bruce Willis as a ghost in SIXTH SENSE. Bad ones do what ME3 did.
And you certainly don't do it with a brand new character. In a good mystery or heist story you might finally reveal the villain's identity at the very end, but their hand should have been felt throughout the story. We should know there's some mastermind out there acting against our heroes. And they didn't do that. I thought Harbinger was our big bad. Nope. Star Child. Huh. Who's that again?
This is bad writing on a technical level. And, it's even more baffling given the 120 hours +/- of truly excellent writing. Worst thing they did was the Arrival DLC, and that still rated 'decent'. These guys don't need Writing 101 instructions. Not when you're producing quality like that.
So, I really, really think that this ending was done with the intent to sell us more DLC. I think it was an executive decision that mucked up our story. And I know enough about how EA does business to know that the producers and writers are under a total gag order to never tell us what really happened.
And, I truly don't CARE what happened. I wanted my emotional payoff that was promised. They didn't deliver. Know what I do to authors who don't give me my payoff? The worst thing imaginable. I stop buying their shit.