This is one of the bigger problems with the ending.
The whole game is about unifying every race. At the end, ghost boy pretty much says none of that matters and that youll still be destroyed unless you pick 1 of the 3 choices. And then Shepard just accepts that depsite the fact that he spent 3 games doing the impossible and find ways to make things work. Now he just goes "welp! thats that" and trudges forward towards whichever colored tube he wants.
I figured from the jump that the ending would boil down a self contained choice, and every single decision leading up to it gave evidence toward that end. Each decision made is in a vacuum with respect to the game, with literally cosmetic changes being the difference between potential consequences. No decision outright influences the game. They all influence you, the player.
So the ending could not be anything other than a decision with respect to how the game influenced you, the player. Through you adventures, your individual person would be biased toward one of the decisions based on the impact the results of your decisions left upon you, and just your own beliefs as a person.
Where I feel Bioware dropped the ball, however, is the explanation of a god-like being granting Shepard this decision, and all the retarded shit that follows. It's not hard to comprehend--it even makes about as much "sense" as the rest of the game--it's just jarring and quite unnecessary. The resolution with TIM ended unsatisfactorily as well. He turned out to be Saren-lite.
The major problem is that Bioware wanted to leave fans speculating, but it had quite the opposite effect. There is no mystery to what happened. No tidbit or incongruity that leaves open potential plot strands or gives depth to the universe. It's just a boring overwrite that shares no thematic consistency with the rest of the Mass Effect universe. It's just something that happens, really. RoboGod told Shepard shit's about to go down, the Reapers just reap, deal with it. Only reaction you could have is "whatever." There's nothing more to go one, and the stakes are merely handed to you out of thin air almost.