Here is my take on things. Aside from what everyone else already explained I have an issue with the vast discrepancy in quality that the endings present: You may have already seen many of these points in some excellent reviews of the endings out there. I will not generally outline the reviews - a particularly good one in my opinion is the Gamefront one - look it up.
1. Let's for now assume that the endings as they are were the definitive and final intent of the developers. Then the number of oversight ERRORS in the endings become very curious since before that and in the previous games the developers have shown exquisite attention to detail.
a) After the blast from Harbinger Shepard loses his armor and appears very bruised but with impeccable uniform! It is understandable that s/he has only a pistol, but darn if the blast destroyed the armor and bruised her/him all over, why is the uniform so clean and sound? And it is hard to imagine that someone (who?) removed her/his armor while s/he was unconscious.
b) What elevates the oversight here is that in the super ending after Shepard chooses the red ending (destroying all synthetics) s/he is shown to survive. But somehow someone put her/his armor back!
c) The whole issue with the people who are shown to survive on the Normandy after the destruction of the relays. How come the love interest is always present regardless if you took her/him to the final assault, in which as you hear on the radio NO ONE else survived... And how did they go to the Normandy if they survived somehow? And why are they running away through a mass relay?
These horrible oversights are creating the feeling that the endings as presented are of significantly lower quality than any other part of the game. That is in addition to all other philosophical and game lore points presented in various articles.
To me it just doesn't make sense that the developers would be satisfied with it. It's mind boggling.
Of course a lot of people are subscribing to the indoctrination/hallucination theory that rather nicely explains the oversight if it were intended by the devs. What irks me personally is that according to my interpretation of Dr. Muzyka's statement the current endings were the intended ones... Unless that is also part of the indoctrination spiel Bioware may be playing - but that becomes more and more implausible...