There are so much theories going around that Shepard becomes Indoctrinated at the end. During the events of all 3 games Shepard has spent
a lot of time around Reaper tech, such as Soverign, numerous artifacts, the Human Reaper, 2 Reaper destroyers and that thing from "The Arrival".
There's a lot of weird things that happen thoughout the game such as Vega saying "You hear that hum? Is it just me?" which is an incredibly strange thing for a guy whose spent a majority of his life on ships to point out. The only other time someone pointed out something weird like that is if you talk to Kaidan near the Relay Artifact on the Citadel, which turns out to be incredibly important at the end because it's a small Mass Relay.
Things like the kid, who disappears as soon as Anderson appears (and
there's a weird Reaper growl when it happens, like in the novels when Greyson resists the Reapers) and who everyone for some reason ignores when he's getting into the shuttle. Then you see shadowy figures and hear whispers in Shepard's dreams (like people who had been indoctrinated sayng they hear voices), and the kid is highlighted by a Reaper light when you approach, and when you finally catch him both you and him are engulfed in flames. Then at the end the kid appears as the Catalyst, and for some reason wants you to pick the 2 options that'll let the Reapers survive, and TIM's choice is blue and Anderson's choice is red. That should be the opposite way around, heck Shepard says to TIM you can't control the Reapers just beforehand.
Anyway there's so much evidence that points towards Indoctrination, just read this, if you can sit down and read through that first post it's really worth it:
http://social.bioware.com/forum/1/topic/355/index/9727423/1
So yeah I didn't mind the endings, but I have to admit I love this theory too. Pretty much everyone is now waiting for Bioware to elaborate, and people suspect ending DLC of some sort.