The main issue that people had with the ending was that your choices seemingly made no difference. You didn't get to see if curing the genophage would cause problems, you didn't get to see if the geth lived peacefully with the quarians, you didn't get to see if you did the opposite choices. Everybody got the same ending regardless of your choices so you might as well have played the game blindfolded and picked random choices.
I normally have no problems with open endings (i.e. in movies/games) but not only was it an open ending, but it was unfulfilled as well.