Okay, I beat the game: the last boss battle was a bit too video gamey, but better than the final form of Saren.
I'm going to finish up the side quests I had left and then start my FemShep Renegade play through.
Here's what I think happened regarding your spoiler:
Since you didn't use that character, you didn't invest squad points into that person's skills, so that might have made it easier for that character to die. Plus, you might not have done research into stuff like tech skills or armor, which might have had something to do with it.