1. Despite the series being based on players being able to make different choices that affect the story, almost nothing the player does throughout the series affects the ending.
2. Although players have a choice of 3 different options during the ending affecting the fate of the galaxy, the only thing that changes in the following cutscenes is the color of some explosions (green for one choice, red for another, blue for the last)
3. The ending felt like a deus ex machina and wasn't satisfying
Lots of fans have expressed their criticism on-line, with many hoping that Bioware will "fix" the ending or release a DLC that alters or extends the ending. This is Bioware's first response as far as I know.