*Spoiler*
Er, in regards to the Indoctrination theory crap:
Does anyone have an answer for why the prothean VI doesn't pick up on Shep's indoctrination?
If every time he sees the kid he's at least partially indoctrinated, including the beginning on earth, then why doesn't the VI notice it on Thessia or the Cerberus Base?
If Shep wasn't experiencing any signs of indoctrination, then the theory falls out the window, since Shep was 100% indoctrination free on the Cerberus base, but is suddenly indoctrinated less than 24 hours later on Earth. To quote the codex:
"Rapid indoctrination is possible, but causes this decay in days or weeks. Slow, patient indoctrination allows the thrall to last for months or years."
So if he is indoctrinated, and it is "rapid onset indoctrination," then that means you have an insane or mentally degraded Shepard to look forward too when he "wakes up" in the Deep Breath cutscene.
Wonderful... Remind me again why this theory gives people so much hope?