Some of ME problem was that it was the end of a beloved trilogy, and if you have noticed they are never usually as popular as the previous installments just because they are the story that brings about the end.
Alien 3, Matrix Revolutions, ROTJ, ROTK, etc.
None of the movies are bad, but I know very few people who prefer those installments over others in the franchise.
My major gripe with it was actually the exclusion of characters from the previous installments. Jack was my love interest in the second game and there was a basic exclusion of her character in the third game.
The dark energy ending isn't necessarily ruled out even with a ending featuring mass relays and reapers.....seems kind of like an intentionally misleading quote to ensure that if bioware needed him to write for something again he could come back.