As far as the *special snowflake* thing, I don't mind it so much. In order to tell a grand story, you need a grand protagonist. Generally, that means the PC ends up being that role. As intriguing as it may be to read a story told from the perspective of someone in Dr. Chakwas's position on the Normandy, imagine playing as that PC. What a dull game! While I might spend $10 or so on an indy playable novel with that idea behind it, there's no way it's a $60+ AAA title.
Let me play the grand protagonist out doing the important things. I am paying for that degree of excitement.
As for the AI theme. If we must have them and you must have the AI trying to be a "real boy" ... at least take it in interesting directions. Why must the AI always turn out good? Can't our "real boy" grow into a some kind of sociopath or some other interesting outcome? What if EDI broke up with Joker and became HAL or the crazy ship from Futurama?
As for human-centric, if you make me feel guilty for being human after you deliberately chose a human protagonist. I am done and so is Mass Effect for me. Tired of being shamed for what I was born.
Now, I don't want so many daddy issues. There are plenty of ways characters can be messed up without having their mommy or daddy involved. TV Tropes has a list of them I think.
Please use the opportunity of having to establish colonies in Andromeda to let us move among the other races' cultures so we get a more alien and less cosmopolitan feel.
Please no antagonist that can only be defeated by a giant contraption you find at the 11th hour that creates explosions in one of three player picked colors, not even if you have those colors be purple, orange and yellow.