It annoys me that people defend this ending. Its bad. Not "well art is in the eye of the beholder" bad, its just plain bad. Not because the ending was depressing, or even filled with plot holes. Its because it didn't do the one thing, THE ONE THING, that an ending is supposed to do. This is called "resolution."
Yes, it resolved the plot with the Reapers (albeit it in a completely awful way). However, it did not resolve the plot with: the Geth, the Quarians, the Krogans, the Turians, the Salarians, the Drell, the Hanar, galactic civilization as a whole, Tali, Liara, Garrus, EDI, Joker, James, Steve Cortez, Javik, Kaidan/Ashley, Aria, Kal'Reegar, Captain Bailey, the Council, Urdnot Bakara, Grunt, Zaeed, Kasumi, or any of a myriad array of other characters whom we've come to know and love.
They spent three video games focusing on the characters with a nice, standard Space Opera plot going on in the background, only to end it abruptly and incompetently. If Return of The Jedi had ended as the core of the second Death Star exploded, if it just cut to credits right there, I can assure you that every patron of every movie theater that played it would stand up, shout WTF?! and walk out. If the Lord of The Rings had cut to credits as soon as the ring fell into the fires of Mt. Doom, no one would have enjoyed the series.
If you say that these endings are good, then you are a sheep. This was not a good ending to Mass Effect, not subjectively, objectively. The opinion that the ending was "good" is objectively wrong. Yes, opinions can be wrong. In fact, many opinions are wrong. The opinion that the average romance novel is good fiction is wrong, just as the opinion that this ending to Mass Effect was wrong.
If Bioware was going for the Indoctrination Theory (which honestly, they should have just gone with, saying "we're really REALLY sorry we didn't fit the ending ending onto the disk, and will be giving it to you free of charge") then this would have been one of the most amazing pieces of writing in a series that has continually shown it can produce such writing.
Instead, we got "pick your color, because the endings are either do what the indoctrinated Illusive Man wants you to do, get rid of all diversity in the galaxy, or kill the Reapers and your synthetic allies. Oh, and heres a few plot holes to go with that."