That was the true ending. I think people find it upsetting becauseWarning: Spoiler! (Click to show)
The game was hyped up as the point where Big Boss turns evil, one of the more important parts of the MGS backstory. People expected to see an epic part of the story and meet some important characters; instead it happened in the background.
Imagine if George Lucas told us Darth Vader wasn't really Anakin Skywalker, but some dude Anakin Skywalker found and brainwashed to be him. I know the prequels weren't good anyway
, but fans would feel extra cheated.
Personally I think the ending is cool and see where Kojima came from, but also why it's so upsetting.
Also YouTube mission 51, the mission they didn't have time to finish. If they put that I there (plus maybe more after it), the story/cutscenes would've ended up having more of an MGS feel. The mission style definitely took some storytelling out, but I think there's a lack of a true MGS climax so that affects it as well.