It came out of no where because it was off the top of my head. It was only a comparison. Nothing else. (Regarding the biblical comparison only). As for the Geth warring against themselves. I actually don't have an answer for that. The Heretics worshiped the "Old Machines", whom they saw as gods. That was the reason given for being the main enemies in Mass Effect 1. Much like the Inusannon's originally supposed to be the Protheans, a storyline which was dropped later in the series in favor for the other Protheans (The Inusannon's were changed to be the Protheans for the Protheans, they are the ones that the Protheans took their technology from). They also inhabited Ilos and you go their their ruins near the end of ME. I could be wrong here, but the change was to point that the Reapers were required to keep peace or dominate races like the Protheans would have complete control over the Galaxy. Off topic. Another ancient race that was supposed to play a more significant race and was forgotten in the sequels was the Thorian, who were basically ancient humans. I don't think they are related at all, but they are very similar.
I think the whole fact that you need high war assets to get the synthetic ending (brining people together is a major part of that and making peace). Is another hint toward my point. This is just my take. But again, it's a new age philosophy thing >.<
I agree with what you are saying about a lot of things not making sense. The whole just being groggy doesn't add up. Such as waking up in an area that happens to look very much where he/she was knocked out. By dream sequence theory, are you referring to indoctrination? Or more on the line of the death and find peace theory. As for the dreams Shepard had. That was part of the Indoctrination ending. Which was cut. Again, the ending was made just prior to release, most of the content was left in. Take it or leave it on that. As for the Indoctrination theory. Even though it's cut, and BioWare won't confirm or deny it publicly. One reason for this is because the official ending was meant to be interrupted in any way you want it to be, it's YOUR story. So in that sense, if you believe in the indoctrination theory, it remains true to that particular player. But in reality, no it's not, it's content that was unfinished and cut to meet the release date. Just like the Illusive Man fight and a few other things. Taking evidence from earlier in the game is what keeps the theory alive and well, even to this day.
I have no reason why it was in both version. The extended cut in my opinion, was terrible. It removed the sense of mystery and tarnished it a little. Most of the significant stuff was presented as still frames.... ugh. I didn't feel like it added much to the story nor the ending, a lot of people on the contrary enjoyed it.
I need to disagree about the ending. It is very basic game design choice. BioWare often makes the dialogue wheel (not always) have a paragon choice on the top, and renegade on the bottom. BioWare again, try's to present it clear. If BioWare wanted to red ending to be canon (in their eyes) They would have had the player directed to it, being the middle choice. Things would obviously, have been built differently with that in mind. If we were to take the rule of thumb. Red is renegade, and blue is paragon. Often you need to do more work for paragon (and on seldom occasions extreme renegade options). So Destroy is technically the bad ending. This is irrelevant either way because there is NO canon for Paragon or Renegade. This is why Shepard is excluded from the graphic novels, which are stated as essential to the canon, equal to the games. Back to my point. BioWare heavily implies direction in their level design. Trying to point where to go, in this sense. It is highly more likely than not to consider that BioWare was pointing out to the player that the Synthetic ending is the best ending. I don't see why it isn't when BioWare considers it to be. It's all in the eye of the beholder and it's your story, but they created the story and to them, that is the ending. Which is funny because it practically is contradictive in its on way. It's up to the player, but to the developers, their story is Syntheses. Hence why they don't flat out state it. Which is why it's so frustrating for me to explain it, especially with the destroy ending being the basic default ending for the lazy shoot em up gamers who run through the game just "killing shit". Which make's killing the Reapers make more sense to them. The majority of the players actually went with the destroy ending (pushing the polls from the forums aside). It's so one sided that it's ridiculous to even consider it a real ending. The control ending is practically admitting that the Illusive Man was right. I don't even understand why it's presented as a "blue" (suggestive paragon) ending, at least it's not genocide on a race. The only ending that is considered morally correct is unifying everything into one, retaining individualism, and tying up the whole "uniting the galaxy" theme. Something that was major. It becomes organics and synesthetic rather than organics vs synthetics. This is a HUGE difference. Ugh it's so frustrating >.<