- The ending story.
- The ending battle.
- The ending cinematic.
- Ending plot holes
When Shepard discovers the meaning behind the Reapers, the story conclusion is a tad disappointing, however I wouldn't consider it repulsive. I had heard that one review said the ending was very similar to "it was all just a dream". It's certainly not that bad. I recall the ending to one game (I think Grandia 3) where the end boss said his goal was to "destroy love". Now that's an awful ending.
Perhaps the ending could have been tweaked to be similar to the Matrix Reloaded. Shepard could have been told the true nature of the Reapers and chosen to let the Reapers continue their destruction, perhaps in exchange for saving his and his crew's life. That certainly would have made the ending story choice more interesting.
I'm not going to rag on Bioware too much for the story ending. With the end of the Mass Effect trilogy, no ending would please all of the fans. The ending to the story was average and acceptable in my eyes.
I think fans have a legitimate gripe here. After playing the game for 20-30 hours, and taking on various side missions to gain "war assets" for the final battle, the end battle appears to be unchanged based on your decisions. During a final battle in which you are protecting some missiles, you could have had some help from Geth, Quarian, mercenaries, Salarian, etc. forces based on your decisions in the game. Perhaps Grunt, Samara, etc. could have come to help as well. However, none of that happened. It was all just on you.
As a comparison, lets look at another Bioware game, Dragon Age: Origins. In the game, you are similarly trying to ally races/people to battle the Darkspawn. Based on your decisions in the game, you can have extra/different allies help you in the final battle (elves, golems, mages, etc.). It makes your decision making in the game more meaningful.
Given Bioware's history of having the game's story affect the end battle, I would say Bioware did drop the ball here. It is certainly not what people expected of a Bioware game.
This is where I think fans are the most irate. Regardless of your decision making at the end, the end cinematic is largely unchanged. There are minor differences, such as the Reapers leaving earth or being destroyed, but 80-90% of the cinematic is identical regardless of your choices.
I wouldn't say Bioware dropped the ball here. In previous games by Bioware (that I can recall), the ending cinematic hasn't been gloriously different either. Even other contemporary games, such as Fallout 3, have had only minor differences in the cinematic ending too. It's hard for me to say that it was something expected by fans.
This isn't to say Bioware couldn't/shouldn't have done better. For example, they could have added an extra 30-60 second cinematic at the very end to show how your decisions affected the world. If you didn't cured the Genophage, perhaps a look 100 years in the future show the Krogan have started a new war with the Salarians. Or perhaps if the Geth and Quarians didn't make peace, a new organic vs. synthetic war occurs.
Well, I think Bioware definitely messed up here. Especially with the ending crash of the Normandy on another planet. How does your crew end up back on the Normandy after your battle on Earth? Especially given some members of your crew were blasted in the final fight.
So overall, do I think Bioware blow the ending? I wouldn't say they did. Fan expectations were through the roof for this game. I imagine some amount of disappointment was bound to occur. However, Bioware could had a number of embarrassing goofs and definitely should have done better.
I would say the disappointment was similar to the disappointment for Dragon Age 2. A quote from RPG site  said, "the discussion about Dragon Age II doesn't need to be "is it good?" - It is - but needs to be "is this what fans wanted from a sequel to Dragon Age: Origins?"
The same can probably be said about Mass Effect 3. The game is really good, that's not in question. But is the ending what fans were expecting? The answer seems to be an emphatic no.
 - http://pc.rpgsite.net/reviews/267-dragon-age-ii-review, through Wikipedia
Ok, I've now learned about the "Indoctrination Theory" for the ending of Mass Effect 3. The theory is really interesting. If it's true, it's actually brilliant, but mean. After giving people a massive game of "choices" and "decisions", you end the game saying, "Aha, you actually did not control your decisions. This is a video game."