The backgrounds should have been very important in the final game, perhaps more so than at any other time. It would have been nice to see specific missions relating to them. A few examples.
Why was a Colonist not even slightly concerned about about their home world. Why not a rescue mission to Mindoir to save some old friends.
Torfan is being used by the Reapers, so Shepard has to go in again. Perfect opportunity to have some flashback play to the original mission.
Have an Earthborn Shepard recruit their old gang as extra troops when on Earth.
I think backgrounds should be the least mentioned in the final game. Who cares if the Shepard is from Mindoir or butchered his squad on Torfan? It isn't important in the large scale of things. Reapers attack and the one who rallies the races is the Commander Shepard, first human Spectre, captain of the Normandy, saviour of the Citadel. That's what's important, not Shepard losing his family on Mindoir or getting his squad killed on Torfan many years ago. Missions like that would've been only important to Shepard, be personal and disconnected with the main plot.
Such missions could fit in ME2, when there is less rush and you can spend ages scanning planets.
As you mentioned in the opening of your post, what you liked was the illusion of being in that world. Surely that would have been strengthened by the game tailoring itself to your Shepard to a small degree?
I would not want game being tailored to the protagonist. That's one of the things that are good about ME3 - despite spearheading the fight against the Reapers you are still just a small detail in the huge war machine. Your indifference can impact you negatively, unlike ME1 and (to a lesser extent) 2.
Intent is very important when picking the lines. For example am I whispering sweet nothings to Thane in ME2 because Shepard is truly in love with him, or is he just a distraction until I can get jiggy with Kaidan again in ME3. Scenes may play out the same but it is the intent of the player that truly gives them shape.
I agree, but you don't put that intent into a paraphrase, you put it into the actual spoken line.
As I mentioned before the failed, and then the fixed but not quite, face imports also helped break the illusion that the previous games had built up.
It was just a minor annoyance to me, I had the face code saved 