Honestly I think your question can be summed up with because their would be no game otherwise.
That's not a good excuse for ignoring the main plot of the first game.
I wonder if they're going to release some sort of 10th Anniversary Special Here's What Really Happened And Oh Remember Those RPG Elements We Had At One Point Say Goodbye To Them edition of the first game to bring it into line with the second two.
I would totally buy a remake of ME1 with ME3's game engine and RPG systems, because the game mechanics were total shit. The fact that they had to scrap the entire thing and rebuild from scratch for ME2 is all the evidence one needs for that.