That's already been covered. Your choices with TIM affects whether Shepard lives or not in the end. Your choice of romantic companion affects who steps out of the Normandy. Your total score at the end affects which ending you can choose, and how battle is progressing and what's back on Earth. Yes, the options are limited compared to all the choices you had to make throughout the series, but like I said before, those choices were resolved outside of the final sequence.
Ok, so let's see... "Your choices with TIM". Um, yeah, ok, the choice you make
at the end of the game affects the end of the game. Yeah, real winner you've started with. And how do any of your previous 3 games worth of choices affect that?
Your choice of romantic companion affects who magically spontaneously teleported on to the Normandy at the end. Yes, very believable, considering said romantic companion was last seen charging the beam with me in London.
And your total score... The
only thing that has any impact at all. And considering that "your score" has no real reflection on your choices, just on how much effort you put into system scanning and multiplayer, that's barely a choice at all.
In other words, your choices have no measurable impact on the game ending.