Uhm, spoilers ahead.

• It’s decent. I would rather have the debates and the theories than another ending.
• I liked the Stargazer postscript too. It just hit some nerve.
• The complaints that the endings are too similar seem flawed. First, since there is only one story, mine, there is only one ending. This may be different for people who play multiple characters. Second, the endings were actually very much different, conceptually. They were just visually identical, and I wonder whether this is the real source of the disappointment. Had Bioware created distinct ending sequences, would people still think them to be the same?
• Certainly, the ending montage is quiet short, and does seem a bit on the cheep. For a 100+ hours trilogy, a Lord of the Rings-type ending seems appropriate. No doubt that some scenes of your war assets in action would have elevated those to more than just point grinding.
• At this point, the Matrix-like Guardian of the Universe character reveal may have become just a bit old now.
• I see an open ending right after the Illusive Man conversation, with Shepard and Anderson staring into space. Mass Effect might just not be that type of story though.

The indoctrination theory is interesting, but in the end, I don’t buy it. The color-coding argument seems fundamentally flawed. The destroy option is red because destroy is simply the Regengade choice. The control option is blue because control is the paragon choice. Anderson may otherwise be a Paragon, but he and you have been working towards a goal, which, in the dichotomy of this choice, is the Rengeade goal. Shepard sees the Illusive Man as executing the Control option, not because he is a Paragon, but because Control has always been the Illusive Man’s choice.

My doubting the theory nonwithstanding I would point to this article for a rebuttle of some of the criticism of the ending.