I'm kind of torn about the ending. The plot holes and other issues already covered extensively leave me quite puzzled. For example, on the final mission, Liara was with me (my love interest as well). When I woke up dazed and struggling, I heard the message everyone was killed. It was actually a very emotional moment, as I realized I had just signed my lover's death warrant. It was my fault she was dead. But luckily she was magically transported to the Normandy. (?) Whew. There are certainly holes in the plot and some flaws in the story and writing, but the more I think about it, and I am afraid to say this...
I like the ending. Not that I think it is perfect, but it doesn't enrage me.
I do believe that Bioware did not live up to promises made to fans. The image on the first page and the quote with it sums that up much more eloquently than I could ever hope. I am very invested in the Mass Effect story, and like many fans, after playing several playthroughs and learning all I could about the universe, played a final time from ME1 all the way through ME2 to build my "canon" Shep for ME3, ready to see "my" ending. At first I hated the end. I reloaded and tried a different end. Then the third. And I couldn't believe nothing changed! I was angry, let down, and confused.
It was the same way I felt when I finished the Dark Tower series. It seemed innapropriate and cheap. But the more I thought about it, the more the end made sense.
I began examining the ME3 story the same way. The end of the game isn't the end of the story- the entire game is the ending of the story. In fact, I think Shep's story ends before he or she gets to the Citadel. After that is an epilogue- the consequense of Shep's journey. Maybe the complexity of having so many endings was more than Bioware intended, and as they began the project, they had the best intentions that reality eventually denied. But as I looked back on my playthrough of ME3, so much of the story was wrapped up in mostly satisfying ways. A couple moments were incredible. Mordin's heroic death stunned me. Having Rachni workers for the crucible justified my belief in not exterminating the species. And so on.
When I got to the Citadel at the end, I did feel like Shep had impacted the Galaxy in truly heroic and epic ways. The story had ended. There was only one more thing...
I would have liked more variety, to see more of what happened after, to have an end that left the remains of civilization with the relays, etc. It did feel a bit like a "kobayashi maru" scenario- my choices really didn't matter. And having one end where Shep could have lived in the face of insurmountable odds would have been hugely satisfying.
But I thought about watching Shep fading away next to Anderson, when Hackett comes on and Shep says, "What do you need me to do." What a heroic drive! And then there was no "Win now" button- it seemed like a dead end! It couldn't possibly end like that...
Who invented the "child?" and other questions would be nice to have answers to, and I think much of the disappointment in the ending stems from the fact that most fans didn't want just a good ending, they wanted an ending that a) explained what happened,

finalized the story in detail, c) was unique to their Shep, and (maybe) d) allowed a "happy" outcome to reward Shep for his or her hard work. They wanted the story wrapped up neatly.
But I don't think the story is about Shep, it is about Shep's impact on history. Throughout the games, you have never fought for fame and glory. You have fought for freedom and survival. You accomplished something that not even countless races could accomplish, and broke the cycle.
There are definitely let downs in the ending, but I think mainly because the ending didn't fit with my own preconceptions. Before the ending, I had so many stories and possibilities in my head, and that made the story even grander than it actually was. A good story does engage the reader or viewer to participate (not in the sense of playing a game, but in creating and filling in between the lines).
I want to say again- my main disappointment with the ending and with the game is that Bioware did not deliver a truly "unique" experience. I felt that while the storylines and my actions were wrapped up, and I got to see many consequences of my actions, and it was satisfying to see them, it left me feeling I had merely played a good, fun game- not that I had completed a unique and epic journey.
ME3 as an entire game is a nice finale to the story. I do wish that the ending was a bit different, but I wish that about many stories. Lost, BSG, Sopranos, The Dark Tower series... But I feel like Shep was a true hero.
You will notice in this post I have never said "my Shep." As I just said, I felt that Shep was a hero, but that it didn't really matter that it was "my" Shep- Shep was a hero with or without me. That is the biggest disappointment.