Here's how I see it.
The fact that the game came out is big news because the game was in development for so long, but in response, the people who were waiting and listening to the 12 year hype for DNF overlooked how nasty a development time the game had when it came to reviewing it, and also what era of gaming this title came from and who it applied to. That I believe explains the negative slants aimed at the character of Duke, because he is quite an old character.
However, I've seen reviewers point out Duke doing puzzles when he supposedly "shouldn't be" (Angry Joe), even though there were plenty of puzzles in the old Duke games and in Duke 3D that you had to do. Then, others have complained about the crude, chauvenistic machoism of Duke as childish (The Escapist), even though that's how he always was, even in the days of Duke 2, which I still love. That said, Yahtzee himself said before that "all reviews are subjective personal opinions", and that "...if you personally enjoyed a game, [bad reviews] really shouldn't get to you."
Having played some of DNF myself, and had a ton of fun and a lot of good, if crude, laughs in the game, I would say that this game fits right in with what I expected from Duke. It does have problems that do deserve to be pointed out, like the loading times, weapon limits, and the loss of extras like hidden areas. Outside of those things however, the game is enjoyable as an FPS, and the Ego Meter can be explained just like that; it's Duke's machoism keeping him alive and stitching those bullet wounds up without the use of anything besides beer and steroids. And what's wrong with that?
Overall, the hate against Duke is just founded on bad expectations and people forgeting the kind of person he was.