Thinking about my sacrifice, for all my friends, etc. got me really teary eyed. Then I thought about my love interest (Liara, who I think they did a GREAT job building our relationship through all 3 games) and how she'd handle things with me gone, etc. It was just extremely emotional for me. As for everything post-that, with people emerging from the Normandy, etc. well, that's probably my biggest confusion, and as for "omg how they here and now there?" that wasn't even a concern. They weren't WITH you during the charge on the beam, they could've been back with the others, maybe I told them to go back to the ship, or something else, who knows. It's weird, but it didn't seem implausible that they escaped Earth somehow during all the madness. It's hard to say how much actual time passed between getting shot and then being dead and then all the other stuff that happened. The people are based on who you use the most, so... if you brought your favorite characters to the final area, then, yeah it could be immersion breaking, in which case I'd blame the game mechanic that decides on who emerges from the Normandy than anything else.
My biggest question with the Green ending is pretty much "What the hell happened to everybody else on the Normandy? Was my sacrifice for a bunch of fucking nobodies that I don't know in the future, or were they also inside the ship but just didn't emerge? I dunno, that'd definitely rub me the wrong way if the endings pretty much all result in 90% of my friends/crew/etc. dying, no matter what.
As for Anderson... Anderson was there for dramatic effect, and because Marauder Shields hadn't shown up yet to protect the gate. He could've woken up well ahead of Shepard and made his way inside with no resistance. As for the Child... I guess he kind of looked like the dream kid. I'd say that was more just coincidence or them trying to be all symbolic, or maybe he was just representing himself in a form that Shepard would recognize? I dunno, those are my guesses there.
A lot of those big issues with the ending seem more like "stylistic" things that can break immersion, but they weren't nearly as bad as Resident Evil 5's ending, so... hey, at least we got that.